My colleague Eleanor Stanley has been using a variety of scripts to clean up the output files from the Maker gene prediction software. She has bundled them together in a shell script (/nfs/users/nfs_e/es9/pipeline/clean_maker_genes.sh).
This script runs several scripts written by me and others, to clean up Maker's final output gff file (round3.nofasta.gff.gz).
The scripts it runs are:
(i) ~es9/pipeline/contaminants.sh - splits the gff file into contaminated and non-contaminated gff files [input: round3.nofasta.gff, output: no_contaminants.gff]
(ii) ~es9/pipeline/remove_contaminant_from_gff.py - removes contaminated contigs from the gff file
(iii) remove_modelgff_genes_from_gff.pl(my script) - removes genes that are remnants from round3 gene training [input: no_contaminants.gff, output: A.gff]
(iv) rename_genes_in_maker_gff.pl (my script) - renames remaining genes [input: A.gff, output: B.gff]
(v) remove_tiny_genes_from_gff.pl (my script) - removes tiny genes that encode proteins of less than 30 residues [input: B.gff, output: C.gff]
(vi) find_best_nonoverlapping_genes.pl (my script) - remove the lowest scoring (nearest to 1) gene in an overlapping set (0 is the best score) [input: C.gff, output: D.gff]
(vii) merge_overlapping_exons.pl (my script) - merge overlapping/consecutive exons [input: E.gff, output: E.gff]
(viii) rename_genes_in_maker_gff.pl (my script) - renames remaining genes [input: E.gff, output: final.gff]
(ix) ~es9/pipeline/make_embedded_gff.sh - run eval
(x) get_spliced_transcripts_from_gff.pl (my script) - make protein sequences [input: final.gff, output: transcript.fa]
(xi) translate_spliced_dna.pl (my script) - make protein sequences [input: transcript.fa, output: protein.fa]
(xii) ~es9/pipeline/intstop.sh - final internal stop codons, if there are any
(xiii) maker_gff_find_incorrect_gene_merges_splits.pl - report genes that are potential splits and merges
Tuesday, 27 August 2013
Friday, 23 August 2013
Basic Python 3 for bioinformatics
Editing a Python 3 script
Type on the linux command-line (note to self: I did this on farm3-login, after logging in which ssh -Y):
% /software/python-3.3.2/bin/idle3
This will open up the 'idle' program:
Then go to the "File" menu in idle, and choose "New Window".
In the window that appears, you can then open an existing Python script by going to "File" and choosing "Open". For example, you could open my Python module haemophilus1.py. You'll then be able to see it within idle (this picture shows just the start of the file):
You can then edit this script within idle if you wish.
The following is a brief selection of simple bioinformatics analyses that you can perform using Python. It was inspired by the Matlab Haemophilus tutorial available on the website for the 'Introduction to Computational Genomics' book.
A Python3 script to retrieve a sequence from GenBank
For example, you could try running this haemophilus1.py script that does this.
To actually run the haemophilus1.py script, you need to type on the linux command-line:
% python3 [Note to self: I ran this on farm3-login, after logging in with 'ssh -Y']
This will bring up the Python prompt, for Python 3.3.2:
You can then load the Python module haemophilus1.py by typing on the prompt:
> import haemophilus1
We know that the GI number in the GenBank database for the Haemophilus influenzae genome sequence (accession NC_000907) is 16271976. Let's get this using Python:
> Hflu = haemophilus1.getgenbank("16271976")
Parsing filename gi_16271976...
Get the length of the DNA sequence:
> print(len(Hflu))
1830138
That is, it is 1,830,138 base-pairs.
Note that if you make some changes to the haemophilus1.py file, and then want to reload it into Python, you type:
> import imp
> imp.reload(haemophilus1)
A Python3 script to calculate the composition of a sequence
The haemophilus1.py script can also calculate the base composition of a sequence.
Look at the composition of the nucleotides in the sequence using the basecount function:
> haemophilus1.basecount(Hflu.seq)
{'C': 350723, 'A': 567623, 'G': 347436, 'T': 564241}
See that there are more As and Ts than Cs and Gs. Note the basecount() returns a dictionary (hash table) with the number of As, Cs, Gs and Ts.
Print out the other symbols in the sequence that correspond to sequencing uncertainties (N=any base, R=A/G, Y=C/T, M=A/C):
> haemophilus1.basecount(Hflu.seq,useall=True)
{'K': 14, 'Y': 11, 'N': 46, 'M': 11, 'R': 10, 'C': 350723, 'A': 567623, 'S': 12, 'G': 347436, 'T': 564241, 'W': 11}
Calculate the frequency of each nucleotide:
> haemophilus1.basecount(Hflu.seq,useall=True,calcfreqs=True,verbose=True)
The sequence is 1830138 base-pairs long
The frequency of K is 0.00
The frequency of N is 0.00
The frequency of M is 0.00
The frequency of C is 0.19
The frequency of A is 0.31
The frequency of G is 0.19
The frequency of Y is 0.00
The frequency of R is 0.00
The frequency of S is 0.00
The frequency of W is 0.00
The frequency of T is 0.31
{'K': 7.649696361695128e-06, 'Y': 6.010475712760459e-06, 'N': 2.513471661699828e-05, 'M': 6.010475712760459e-06, 'R': 5.464068829782235e-06, 'C': 0.19163746121877148, 'A': 0.3101531141367482, 'S': 6.556882595738682e-06, 'G': 0.18984142179442207, 'T': 0.3083051660585158, 'W': 6.010475712760459e-06}
Calculate the number of each type of base on the complementary strand:
> haemophilus1.basecount(Hflu.seq.reverse_complement())
{'C': 347436, 'A': 564241, 'G': 350723, 'T': 567623}
Calculate the frequency of bases on the complementary strand, and check that the frequency of As on the complementary strand is the same as the frequency of Ts on this strand, etc.:
> haemophilus1.basecount(Hflu.seq.reverse_complement(),calcfreqs=True)
{'C': 0.18984142179442207, 'A': 0.3083051660585158, 'G': 0.19163746121877148, 'T': 0.3101531141367482}
A Python3 script to make a sliding window of GC content:
Look at local variation in GC content by calculating GC content in a sliding window of size 20000 bp:
[Note: pylab is part of matplotlib (in matplotlib.pylab) and tries to give you a MatLab like environment.]
> haemophilus1.ntdensity1(Hflu.seq,20000,makeplot=True)
A Python3 script to make a sliding window of base content:
Look at local variation in base content by calculating base content in a sliding window of size 20000 bp:
> haemophilus1.ntdensity2(Hflu.seq,20000,makeplot=True)
A Python3 script to calculate the frequency of dimers in a sequence:
Look at the dimers in the sequence and display the 2-mer frequencies:
> haemophilus1.dimercount(Hflu.seq)
{'CC': 68014, 'TC': 94745, 'CA': 121618, 'TA': 131955, 'CG': 72523, 'TG': 119996, 'AA': 219880, 'AC': 92410, 'GC': 95529, 'AG': 88457, 'GG': 66448, 'GA': 94125, 'TT': 217512, 'CT': 88551, 'GT': 91314, 'AT': 166837}
Running the 'doctests' for Python3:
Each of the subroutines in the haemophilus.py module file has a 'doctest'. To run all the doctests you can type:
% python3 haemophilus1.py test
If there are no problems (all the tests pass), you should get no output back.
Python things I always forget
Finding a substring in a string:
> myset = ("A+T", "G+C")
> dimer <- myset[1]
'G+C'
> dimer[0:1]
'G'
> dimer[1:2]
'+'
> dimer[2:3]
'C'
Looping over a sequence of numbers:
> for i in range(0,10)
Goes from i=0...9
Reloading a module (eg. 'haemophilus.py'):
> import imp
> imp.reload(haemophilus1)
Creating a dictionary with two empty lists:
> freqs = { "G+C": [], "A+T": [] }
Then we can store something in the list:
> dimer = 'G+C'
> pc = 10.32
> freqs[dimer].append(pc)
> freqs
{'G+C': [10.32], 'A+T': []}
Type on the linux command-line (note to self: I did this on farm3-login, after logging in which ssh -Y):
% /software/python-3.3.2/bin/idle3
This will open up the 'idle' program:
In the window that appears, you can then open an existing Python script by going to "File" and choosing "Open". For example, you could open my Python module haemophilus1.py. You'll then be able to see it within idle (this picture shows just the start of the file):
You can then edit this script within idle if you wish.
The following is a brief selection of simple bioinformatics analyses that you can perform using Python. It was inspired by the Matlab Haemophilus tutorial available on the website for the 'Introduction to Computational Genomics' book.
A Python3 script to retrieve a sequence from GenBank
For example, you could try running this haemophilus1.py script that does this.
To actually run the haemophilus1.py script, you need to type on the linux command-line:
% python3 [Note to self: I ran this on farm3-login, after logging in with 'ssh -Y']
This will bring up the Python prompt, for Python 3.3.2:
You can then load the Python module haemophilus1.py by typing on the prompt:
> import haemophilus1
We know that the GI number in the GenBank database for the Haemophilus influenzae genome sequence (accession NC_000907) is 16271976. Let's get this using Python:
> Hflu = haemophilus1.getgenbank("16271976")
Parsing filename gi_16271976...
Get the length of the DNA sequence:
> print(len(Hflu))
1830138
That is, it is 1,830,138 base-pairs.
Note that if you make some changes to the haemophilus1.py file, and then want to reload it into Python, you type:
> import imp
> imp.reload(haemophilus1)
A Python3 script to calculate the composition of a sequence
The haemophilus1.py script can also calculate the base composition of a sequence.
Look at the composition of the nucleotides in the sequence using the basecount function:
> haemophilus1.basecount(Hflu.seq)
{'C': 350723, 'A': 567623, 'G': 347436, 'T': 564241}
See that there are more As and Ts than Cs and Gs. Note the basecount() returns a dictionary (hash table) with the number of As, Cs, Gs and Ts.
Print out the other symbols in the sequence that correspond to sequencing uncertainties (N=any base, R=A/G, Y=C/T, M=A/C):
> haemophilus1.basecount(Hflu.seq,useall=True)
{'K': 14, 'Y': 11, 'N': 46, 'M': 11, 'R': 10, 'C': 350723, 'A': 567623, 'S': 12, 'G': 347436, 'T': 564241, 'W': 11}
Calculate the frequency of each nucleotide:
> haemophilus1.basecount(Hflu.seq,useall=True,calcfreqs=True,verbose=True)
The sequence is 1830138 base-pairs long
The frequency of K is 0.00
The frequency of N is 0.00
The frequency of M is 0.00
The frequency of C is 0.19
The frequency of A is 0.31
The frequency of G is 0.19
The frequency of Y is 0.00
The frequency of R is 0.00
The frequency of S is 0.00
The frequency of W is 0.00
The frequency of T is 0.31
{'K': 7.649696361695128e-06, 'Y': 6.010475712760459e-06, 'N': 2.513471661699828e-05, 'M': 6.010475712760459e-06, 'R': 5.464068829782235e-06, 'C': 0.19163746121877148, 'A': 0.3101531141367482, 'S': 6.556882595738682e-06, 'G': 0.18984142179442207, 'T': 0.3083051660585158, 'W': 6.010475712760459e-06}
Calculate the number of each type of base on the complementary strand:
> haemophilus1.basecount(Hflu.seq.reverse_complement())
{'C': 347436, 'A': 564241, 'G': 350723, 'T': 567623}
Calculate the frequency of bases on the complementary strand, and check that the frequency of As on the complementary strand is the same as the frequency of Ts on this strand, etc.:
> haemophilus1.basecount(Hflu.seq.reverse_complement(),calcfreqs=True)
{'C': 0.18984142179442207, 'A': 0.3083051660585158, 'G': 0.19163746121877148, 'T': 0.3101531141367482}
A Python3 script to make a sliding window of GC content:
Look at local variation in GC content by calculating GC content in a sliding window of size 20000 bp:
[Note: pylab is part of matplotlib (in matplotlib.pylab) and tries to give you a MatLab like environment.]
> haemophilus1.ntdensity1(Hflu.seq,20000,makeplot=True)
A Python3 script to make a sliding window of base content:
Look at local variation in base content by calculating base content in a sliding window of size 20000 bp:
> haemophilus1.ntdensity2(Hflu.seq,20000,makeplot=True)
A Python3 script to calculate the frequency of dimers in a sequence:
Look at the dimers in the sequence and display the 2-mer frequencies:
> haemophilus1.dimercount(Hflu.seq)
{'CC': 68014, 'TC': 94745, 'CA': 121618, 'TA': 131955, 'CG': 72523, 'TG': 119996, 'AA': 219880, 'AC': 92410, 'GC': 95529, 'AG': 88457, 'GG': 66448, 'GA': 94125, 'TT': 217512, 'CT': 88551, 'GT': 91314, 'AT': 166837}
Running the 'doctests' for Python3:
Each of the subroutines in the haemophilus.py module file has a 'doctest'. To run all the doctests you can type:
% python3 haemophilus1.py test
If there are no problems (all the tests pass), you should get no output back.
Python things I always forget
Finding a substring in a string:
> myset = ("A+T", "G+C")
> dimer <- myset[1]
'G+C'
> dimer[0:1]
'G'
> dimer[1:2]
'+'
> dimer[2:3]
'C'
Looping over a sequence of numbers:
> for i in range(0,10)
Goes from i=0...9
Reloading a module (eg. 'haemophilus.py'):
> import imp
> imp.reload(haemophilus1)
Creating a dictionary with two empty lists:
> freqs = { "G+C": [], "A+T": [] }
Then we can store something in the list:
> dimer = 'G+C'
> pc = 10.32
> freqs[dimer].append(pc)
> freqs
{'G+C': [10.32], 'A+T': []}
Monday, 12 August 2013
DESeq R package for finding differential expression analysis of RNA-seq data
The DESeq 2010 paper by Anders & Huber
I've just presented the DESeq paper (Anders & Huber 2010) as a journal club paper, and have put my slides on slideshare in case they're of interest to anyone.
The main points of the paper are:
- A Poisson model underestimates the variance in RNA-seq read counts for a gene between biological samples, and this leads to false positives if you are using a Poisson model to detect differentially expressed genes.
- A Negative Binomial distribution is much better, especially for highly expressed genes, where a Poisson greatly underestimates the true variance.
- DESeq and EdgeR both use the Negative Binomial distribution to model the number of RNA-seq read counts for a gene.
- However, there are a couple of key differences between DESeq and EdgeR:
(i) DESeq estimates the sequencing depth for a library differently than EdgeR
(ii) DESeq estimates the variance in read count for a gene by assuming that it will have similar variance to genes of similar expression level (it uses a local regression of genes' variance versus expression, to estimate the variance)
[Note: my colleagues tell me that recent versions of EdgeR and DESeq seem to have changed however, and may do things more similarly nowadays.]
- According to the DESeq paper (which is now a few years old), DESeq and EdgeR have similar sensitivity for detecting differentially expressed genes, but EdgeR calls a greater number of weakly expressed genes as significant, and fewer highly expressed genes as significant, compared to DESeq. [Again, it would be nice to know if this is still the case, since these tools have been changed since publication of this paper.]
- DESeq has a clever way of estimating the sequencing depth for a library, that avoids being affected by just a few highly expressed genes. They say that the total number of reads in a library can be affected by just a few highly expressed genes, so isn't a good measure of sequencing depth. They use their measure of sequencing depth to normalise the estimated read count from a library for a particular gene, to give a more accurate measure of its expression level. My colleague Adam Reid suggested that this could be a better measure of expression level than RPKM, which is based on the total number of reads in a library (and so can be affected by just a few highly expressed genes).
Changes since the paper was published
The DESeq vignette (available here) lists some changes since the paper was published:
- the way in which the p-values are calculated has changed slightly (see the vignette for details)
- the way in which the variances (dispersions) has changed slightly (see below)
- in the original paper, a separate mean-dispersion regression was made for each condition, but in the latest version of DESeq, one dispersion value is estimated for a gene across all (replicated) conditions, and this is used to make a single mean-dispersion regression
- in the original paper, local regression was used to fit the mean-dispersion relationship. In the latest version of DESeq, a parametric regression is used instead by default.
Other nice features of DESeq
Based on reading the DESeq vignette (available here) and the paper, here is a list of other nice features of DESeq:
- It will still work if you only have biological replicates for one condition, and not for the second condition. It will even work if you don't have biological replicates for either of your two conditions (ie. just one biological replicate from each condition), although this is not recommended, as it is based on the assumption that only a small fraction of the genes are differentially expressed between conditions.
Running DESeq
My colleague Anna Protasio suggested that a good way to learn DESeq is to work through the R vignette, available here.
Here are the basic steps, using the example in the vignette:
1) Read in the count data from a file (previously generated):
% R-3.0.0
> library(pasilla, lib="~alc/R/library")
> library(DESeq, lib="~alc/R/library")
> datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )
> pasillaCountTable = read.table( datafile, header=TRUE, row.names=1 )
[Note to self: I ran this on pcs4, by logging in using 'ssh -Y psc4']
The pasillaCountTable data frame has the genes as rows and samples (including biological replicates, but with each set of technical replicates merged into one) as columns. The values are raw read counts.
Note: you can view the pasilla_gene_counts.tsv file here.
2) Store the metadata for the data set:
> pasillaDesign = data.frame(row.names = colnames( pasillaCountTable ), condition = c( "untreated", "untreated", "untreated", "untreated", "treated", "treated", "treated" ), libType = c( "single-end", "single-end", "paired-end","paired-end", "single-end", "paired-end", "paired-end" ) )
We can extract out just the data for the paired-end samples, to keep things simple:
> pairedSamples = pasillaDesign$libType == "paired-end"
> countTable = pasillaCountTable[ , pairedSamples ]
> condition = pasillaDesign$condition[ pairedSamples ]
3) Make a DESeq 'CountDataSet' object for the data:
Now make a DESeq 'CountDataSet' object:
> cds = newCountDataSet( countTable, condition )
4) Normalise the data, by estimating the sequencing depth for each sample:
> cds = estimateSizeFactors( cds )
> sizeFactors( cds )
untreated3 untreated4 treated2 treated3
0.8730966 1.0106112 1.0224517 1.1145888
These are relative sequencing depths of the different samples.
We can normalise the count data for genes, by dividing the raw counts by these sequencing depth factors (this gives the q_i value for gene i in a sample, described in the DESeq paper equation 6), eg.:
> head( counts( cds, normalized=TRUE ) )
untreated3 untreated4 treated2 treated3
FBgn0000003 0.000000 0.00000 0.00000 0.8971919
FBgn0000008 87.046493 69.26502 86.06763 62.8034302
FBgn0000014 0.000000 0.00000 0.00000 0.0000000
FBgn0000015 1.145349 1.97900 0.00000 0.0000000
FBgn0000017 4082.022370 3116.92579 3004.54278 2991.2376629
FBgn0000018 280.610404 306.74508 292.43434 276.3350930
...
This gives normalised expression level (read count) values for the genes. One normalised expression value is given for each gene in each biological replicate.
5) Estimate the variances of the expression levels values for each gene, across all samples:
The variance of a gene is estimated as the sum of two components: the uncertainty in measuring a concentration by counting reads ("shot noise") plus the variation between biological replicates for a condition (called the "dispersion" in the DESeq vignette), as given in Equation 3 in the DESeq paper.
To estimate the dispersion values for genes, we type:
> cds = estimateDispersions( cds )
The vignette explains that the 'estimateDispersions' function carries out three steps:
(i) it estimates the dispersion value for each gene: w_i across all the biological replicates for all conditions (using Equation 7 in the DESeq paper),
(ii) it fits a curve through these estimates, ie. fits a regression line between w_i for genes and the mean (across all biological replicates for all conditions) normalised expression level for the genes (q_i; see equation 6 in the DESeq paper). The vignette points out that in the paper a local regression was used, but by default the latest software version uses a parametric fit instead.
(iii) it assigns the gene a dispersion value. The vignette says that w_i is used if it is greater than the fitted value from the regression, and otherwise the fitted value from the regression is used. The vignette explains that this change has been made since the paper was published, to take into account that some genes seem to have much higher dispersion than others.
The paper says that Equation 8 is used, which subtracts a value z_i from the fitted value. I'm not sure if the z_i values are still used in the calculation, the vignette doesn't make this clear. (?)
Note that in the paper they described estimating a separate dispersion value for a gene in each condition (where there are several replicates for each condition), but it seems that the latest version of the software estimates just one dispersion value for a gene, across all the biological replicates from all conditions.
As a QC step, we can plot the per-gene dispersion estimates (w_i) against the mean normalised counts per gene (q_i), and overlay the fitted curve:
> plotDispEsts( cds )
6) Call differential expression between two experimental conditions ('treated' versus 'untreated' here):
> res = nbinomTest( cds, "untreated", "treated" )
This takes a minute or two to run.
> head(res)
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
1 FBgn0000003 0.2242980 0.000000 0.4485959 Inf Inf 1.0000000 1.0000000
2 FBgn0000008 76.2956431 78.155755 74.4355310 0.9523999 -0.07036067 0.8354725 1.0000000
3 FBgn0000014 0.0000000 0.000000 0.0000000 NaN NaN NA NA
4 FBgn0000015 0.7810873 1.562175 0.0000000 0.0000000 -Inf 0.4160556 1.0000000
5 FBgn0000017 3298.6821506 3599.474078 2997.8902236 0.8328690 -0.26383857 0.2414208 0.8811746
6 FBgn0000018 289.0312286 293.677741 284.3847165 0.9683564 -0.04638999 0.7572819 1.0000000
where "id" is the gene name;
"baseMean" is the mean normalised expression level, averaged over all replicates from all conditions;
"baseMeanA" is the mean normalised expression level, averaged over all condition A replicates;
"baseMeanB" is the mean normalised expression level, averaged over all condition B replicates;
"foldChange" is the fold change from condition A to B;
"log2FoldChange" is the log2 of foldChange;
"pval" is the p-value;
"padj" is the p-value adjusted for multiple testing using the Benjamini-Hochberg procedure.
We can plot log2FoldChange against baseMean, with genes that are significant at a 10% false discovery rate (FDR) coloured red:
> plotMA(res)
Thanks to my colleagues in the Parasite Genomics Team for very interesting discussion about this.
I've just presented the DESeq paper (Anders & Huber 2010) as a journal club paper, and have put my slides on slideshare in case they're of interest to anyone.
The main points of the paper are:
- A Poisson model underestimates the variance in RNA-seq read counts for a gene between biological samples, and this leads to false positives if you are using a Poisson model to detect differentially expressed genes.
- A Negative Binomial distribution is much better, especially for highly expressed genes, where a Poisson greatly underestimates the true variance.
- DESeq and EdgeR both use the Negative Binomial distribution to model the number of RNA-seq read counts for a gene.
- However, there are a couple of key differences between DESeq and EdgeR:
(i) DESeq estimates the sequencing depth for a library differently than EdgeR
(ii) DESeq estimates the variance in read count for a gene by assuming that it will have similar variance to genes of similar expression level (it uses a local regression of genes' variance versus expression, to estimate the variance)
[Note: my colleagues tell me that recent versions of EdgeR and DESeq seem to have changed however, and may do things more similarly nowadays.]
- According to the DESeq paper (which is now a few years old), DESeq and EdgeR have similar sensitivity for detecting differentially expressed genes, but EdgeR calls a greater number of weakly expressed genes as significant, and fewer highly expressed genes as significant, compared to DESeq. [Again, it would be nice to know if this is still the case, since these tools have been changed since publication of this paper.]
- DESeq has a clever way of estimating the sequencing depth for a library, that avoids being affected by just a few highly expressed genes. They say that the total number of reads in a library can be affected by just a few highly expressed genes, so isn't a good measure of sequencing depth. They use their measure of sequencing depth to normalise the estimated read count from a library for a particular gene, to give a more accurate measure of its expression level. My colleague Adam Reid suggested that this could be a better measure of expression level than RPKM, which is based on the total number of reads in a library (and so can be affected by just a few highly expressed genes).
Changes since the paper was published
The DESeq vignette (available here) lists some changes since the paper was published:
- the way in which the p-values are calculated has changed slightly (see the vignette for details)
- the way in which the variances (dispersions) has changed slightly (see below)
- in the original paper, a separate mean-dispersion regression was made for each condition, but in the latest version of DESeq, one dispersion value is estimated for a gene across all (replicated) conditions, and this is used to make a single mean-dispersion regression
- in the original paper, local regression was used to fit the mean-dispersion relationship. In the latest version of DESeq, a parametric regression is used instead by default.
Other nice features of DESeq
Based on reading the DESeq vignette (available here) and the paper, here is a list of other nice features of DESeq:
- It will still work if you only have biological replicates for one condition, and not for the second condition. It will even work if you don't have biological replicates for either of your two conditions (ie. just one biological replicate from each condition), although this is not recommended, as it is based on the assumption that only a small fraction of the genes are differentially expressed between conditions.
Running DESeq
My colleague Anna Protasio suggested that a good way to learn DESeq is to work through the R vignette, available here.
Here are the basic steps, using the example in the vignette:
1) Read in the count data from a file (previously generated):
% R-3.0.0
> library(pasilla, lib="~alc/R/library")
> library(DESeq, lib="~alc/R/library")
> datafile = system.file( "extdata/pasilla_gene_counts.tsv", package="pasilla" )
> pasillaCountTable = read.table( datafile, header=TRUE, row.names=1 )
[Note to self: I ran this on pcs4, by logging in using 'ssh -Y psc4']
The pasillaCountTable data frame has the genes as rows and samples (including biological replicates, but with each set of technical replicates merged into one) as columns. The values are raw read counts.
Note: you can view the pasilla_gene_counts.tsv file here.
2) Store the metadata for the data set:
> pasillaDesign = data.frame(row.names = colnames( pasillaCountTable ), condition = c( "untreated", "untreated", "untreated", "untreated", "treated", "treated", "treated" ), libType = c( "single-end", "single-end", "paired-end","paired-end", "single-end", "paired-end", "paired-end" ) )
We can extract out just the data for the paired-end samples, to keep things simple:
> pairedSamples = pasillaDesign$libType == "paired-end"
> countTable = pasillaCountTable[ , pairedSamples ]
> condition = pasillaDesign$condition[ pairedSamples ]
3) Make a DESeq 'CountDataSet' object for the data:
Now make a DESeq 'CountDataSet' object:
> cds = newCountDataSet( countTable, condition )
4) Normalise the data, by estimating the sequencing depth for each sample:
> cds = estimateSizeFactors( cds )
> sizeFactors( cds )
untreated3 untreated4 treated2 treated3
0.8730966 1.0106112 1.0224517 1.1145888
These are relative sequencing depths of the different samples.
We can normalise the count data for genes, by dividing the raw counts by these sequencing depth factors (this gives the q_i value for gene i in a sample, described in the DESeq paper equation 6), eg.:
> head( counts( cds, normalized=TRUE ) )
untreated3 untreated4 treated2 treated3
FBgn0000003 0.000000 0.00000 0.00000 0.8971919
FBgn0000008 87.046493 69.26502 86.06763 62.8034302
FBgn0000014 0.000000 0.00000 0.00000 0.0000000
FBgn0000015 1.145349 1.97900 0.00000 0.0000000
FBgn0000017 4082.022370 3116.92579 3004.54278 2991.2376629
FBgn0000018 280.610404 306.74508 292.43434 276.3350930
...
This gives normalised expression level (read count) values for the genes. One normalised expression value is given for each gene in each biological replicate.
5) Estimate the variances of the expression levels values for each gene, across all samples:
The variance of a gene is estimated as the sum of two components: the uncertainty in measuring a concentration by counting reads ("shot noise") plus the variation between biological replicates for a condition (called the "dispersion" in the DESeq vignette), as given in Equation 3 in the DESeq paper.
To estimate the dispersion values for genes, we type:
> cds = estimateDispersions( cds )
The vignette explains that the 'estimateDispersions' function carries out three steps:
(i) it estimates the dispersion value for each gene: w_i across all the biological replicates for all conditions (using Equation 7 in the DESeq paper),
(ii) it fits a curve through these estimates, ie. fits a regression line between w_i for genes and the mean (across all biological replicates for all conditions) normalised expression level for the genes (q_i; see equation 6 in the DESeq paper). The vignette points out that in the paper a local regression was used, but by default the latest software version uses a parametric fit instead.
(iii) it assigns the gene a dispersion value. The vignette says that w_i is used if it is greater than the fitted value from the regression, and otherwise the fitted value from the regression is used. The vignette explains that this change has been made since the paper was published, to take into account that some genes seem to have much higher dispersion than others.
The paper says that Equation 8 is used, which subtracts a value z_i from the fitted value. I'm not sure if the z_i values are still used in the calculation, the vignette doesn't make this clear. (?)
Note that in the paper they described estimating a separate dispersion value for a gene in each condition (where there are several replicates for each condition), but it seems that the latest version of the software estimates just one dispersion value for a gene, across all the biological replicates from all conditions.
As a QC step, we can plot the per-gene dispersion estimates (w_i) against the mean normalised counts per gene (q_i), and overlay the fitted curve:
> plotDispEsts( cds )
> res = nbinomTest( cds, "untreated", "treated" )
This takes a minute or two to run.
> head(res)
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
1 FBgn0000003 0.2242980 0.000000 0.4485959 Inf Inf 1.0000000 1.0000000
2 FBgn0000008 76.2956431 78.155755 74.4355310 0.9523999 -0.07036067 0.8354725 1.0000000
3 FBgn0000014 0.0000000 0.000000 0.0000000 NaN NaN NA NA
4 FBgn0000015 0.7810873 1.562175 0.0000000 0.0000000 -Inf 0.4160556 1.0000000
5 FBgn0000017 3298.6821506 3599.474078 2997.8902236 0.8328690 -0.26383857 0.2414208 0.8811746
6 FBgn0000018 289.0312286 293.677741 284.3847165 0.9683564 -0.04638999 0.7572819 1.0000000
where "id" is the gene name;
"baseMean" is the mean normalised expression level, averaged over all replicates from all conditions;
"baseMeanA" is the mean normalised expression level, averaged over all condition A replicates;
"baseMeanB" is the mean normalised expression level, averaged over all condition B replicates;
"foldChange" is the fold change from condition A to B;
"log2FoldChange" is the log2 of foldChange;
"pval" is the p-value;
"padj" is the p-value adjusted for multiple testing using the Benjamini-Hochberg procedure.
We can plot log2FoldChange against baseMean, with genes that are significant at a 10% false discovery rate (FDR) coloured red:
> plotMA(res)
This MA plot has what is called a 'sting-ray' shape by some of my colleagues. There are more genes of higher expression level that are called as differentially expressed, compared to genes of low expression level.
The DESeq vignette also recommends to have a look at a histogram of the p-values:
> hist(res$pval, breaks=100, col="skyblue", border="slateblue", main="")
The lower values are due to differentially expressed genes, while the p-values for genes that are not differentially expressed are uniformly distributed between 0 and 1 (except p-values for very poorly expressed genes, which are close to 1).
To filter for significant genes, according to some threshold for false discovery rate (FDR):
> resSig = res[ res$padj < 0.1, ]
To list the most significantly differentially expressed genes:
> head( resSig[ order(resSig$pval), ] )
id baseMean baseMeanA baseMeanB foldChange log2FoldChange pval padj
9831 FBgn0039155 463.4369 884.9640 41.90977 0.0473576 -4.400260 1.641210e-124 1.887556e-120
2366 FBgn0025111 1340.2282 311.1697 2369.28680 7.6141316 2.928680 3.496915e-107 2.010901e-103
2366 FBgn0025111 1340.2282 311.1697 2369.28680 7.6141316 2.928680 3.496915e-107 2.010901e-103
612 FBgn0003360 2544.2512 4513.9457 574.55683 0.1272848 -2.973868 1.552884e-99 5.953239e-96
3192 FBgn0029167 2551.3113 4210.9571 891.66551 0.2117489 -2.239574 4.346335e-78 1.249680e-74
10305 FBgn0039827 188.5927 357.3299 19.85557 0.0555665 -4.169641 1.189136e-65 2.735251e-62
6948 FBgn0035085 447.2485 761.1898 133.30718 0.1751300 -2.513502 3.145997e-56 6.030352e-53
10305 FBgn0039827 188.5927 357.3299 19.85557 0.0555665 -4.169641 1.189136e-65 2.735251e-62
6948 FBgn0035085 447.2485 761.1898 133.30718 0.1751300 -2.513502 3.145997e-56 6.030352e-53
We can tally the number of differentially expressed genes:
> addmargins( table( res_sig = res$padj < .1) )
FALSE TRUE Sum
10680 821 11501
FALSE TRUE Sum
10680 821 11501
To save the output to a file, we can type:
> write.csv( res, file="My Pasilla Analysis Result Table.csv" )
7) Data quality assessment by sample clustering and visualisation
The DESeq vignette recommends that you carry out some quality assessment steps.
Firstly, you can make a heat map of variance stabilisation transformed data (see the DESeq paper for an explanation of the variance stabilising transformation), ie. a heatmap of genes:
> cdsFullBlind = estimateDispersions( cdsFull, method = "blind" )
> vsdFull = varianceStabilizingTransformation( cdsFullBlind )
> library("RColorBrewer")
> library("gplots")
> select = order(rowMeans(counts(cdsFull)), decreasing=TRUE)[1:30]
> hmcol = colorRampPalette(brewer.pal(9, "GnBu"))(100)
> heatmap.2(exprs(vsdFull)[select,], col = hmcol, trace="none", margin=c(10, 6))
This gives a heatmap for the 30 most highly expressed genes:
You can see that, for these 30 genes, the treated samples are grouped together, and the untreated samples are grouped together.
You can also make a heatmap of the samples, using the variance stabilised data:
> dists = dist( t( exprs(vsdFull) ) )
> mat = as.matrix( dists )
> rownames(mat) = colnames(mat) = with(pData(cdsFullBlind), paste(condition, libType, sep=" : "))
> heatmap.2(mat, trace="none", col = rev(hmcol), margin=c(13, 13))
It's reassuring to see that the untreated samples group with each other, as do the treated samples.
We can also make a PCA plot of the samples, using:
> print(plotPCA(vsdFull, intgroup=c("condition", "libType")))
The first principle component separates the treated and untreated samples, while the second principle component separates the paired-end and single-end samples.
8) Other topics
The DESeq vignette also covers other topics such as:
- what to do if you have multiple factors (eg. condition such as 'treated' and 'untreated', library type such as 'paired-end' and 'single-end', etc.)
- 'independent filtering' (ie. filtering out those tests from the procedure that have no, or little chance of showing significant evidence, without even looking at their test statistic) based on the overall sum of counts (independent of biological condition)
- how to perform a variance stabilising transformation (as described also in the DESeq paper), for example, if you are intending to perform a cluster analysis of the data or to plot the data.
Thanks to my colleagues in the Parasite Genomics Team for very interesting discussion about this.
Wednesday, 7 August 2013
PCR duplicates in Illumina sequencing
PCR duplicates
Here is a nice blog by Eric Vallabh Minikel explaining how PCR duplicates arise during Illumina sequencing.
To summarise, what it says is that an early step in Illumina sequencing is to PCR amplify fragments that have adaptors ligated to each end, which amplifies your DNA about 64-fold. The next step after this is to spread the DNA solution across flow cells, with the aim of getting one DNA molecule per flow cell lawn of primers.
[Note: the DNA molecules are attached at random positions to the inside surface of a flow cell, which is covered with a dense lawn of primers; tens of millions of DNA molecules will attach to the flow cell surface, each will form one 'cluster' when bridge PCR occurs].
However, sometimes you get two copies of the same original molecule (say, 2 out of the 64 copies you made of each molecule) which each stick to a different flow cell lawn, and so you'll be reading the same DNA in two different flow cell 'clusters' [each 'cluster' having about 1 million copies of the original fragment, produced by bridge PCR in a tiny region of the flow cell] - these are your PCR duplicates.
In a seqanswers.com discussion, Li Heng (lh3) says that the rate of PCR duplicates is 0.5*m/N, where m is the number of sequenced reads, and N is the number of DNA molecules before amplification. He said that the key to reducing PCR duplicates is to get enough DNA (large N). The more reads you sequence (higher m), the more PCR duplicates you will get however.
Optical duplicates
In a seqanswers.com discussion, Li Heng (lh3) says that optical duplicates are sequences from one flow cell cluster, that are (incorrectly) identified by software to be from multiple adjacent clusters.
Identifying PCR duplicates and optical duplicates
In a seqanswers.com discussion, Li Heng (lh3) says that PCR duplicates are usually identified after alignment, eg. by identifying read-pairs that have identical 5'-end coordinates.
Li Heng says that optical duplicates can be identified by checking the sequence and the coordinates on the image, and that alignment is not neeed to identify them.
Should we mark (and remove) duplicates from the analysis?
Li Heng says that marking (and removing duplicates) from your analysis is a good idea for SNP calling because you generally have high coverage data. However, he says it is dangerous to mark (and remove) duplicates for RNA-seq or ChIP-Seq where read count matters. He says it would be better to account for duplicates in your read counting model than run a duplicate-marking program.
Thanks to Bhavana Harsha for the link to Eric Vallabh Minikel's blog.
Here is a nice blog by Eric Vallabh Minikel explaining how PCR duplicates arise during Illumina sequencing.
To summarise, what it says is that an early step in Illumina sequencing is to PCR amplify fragments that have adaptors ligated to each end, which amplifies your DNA about 64-fold. The next step after this is to spread the DNA solution across flow cells, with the aim of getting one DNA molecule per flow cell lawn of primers.
[Note: the DNA molecules are attached at random positions to the inside surface of a flow cell, which is covered with a dense lawn of primers; tens of millions of DNA molecules will attach to the flow cell surface, each will form one 'cluster' when bridge PCR occurs].
However, sometimes you get two copies of the same original molecule (say, 2 out of the 64 copies you made of each molecule) which each stick to a different flow cell lawn, and so you'll be reading the same DNA in two different flow cell 'clusters' [each 'cluster' having about 1 million copies of the original fragment, produced by bridge PCR in a tiny region of the flow cell] - these are your PCR duplicates.
In a seqanswers.com discussion, Li Heng (lh3) says that the rate of PCR duplicates is 0.5*m/N, where m is the number of sequenced reads, and N is the number of DNA molecules before amplification. He said that the key to reducing PCR duplicates is to get enough DNA (large N). The more reads you sequence (higher m), the more PCR duplicates you will get however.
Optical duplicates
In a seqanswers.com discussion, Li Heng (lh3) says that optical duplicates are sequences from one flow cell cluster, that are (incorrectly) identified by software to be from multiple adjacent clusters.
Identifying PCR duplicates and optical duplicates
In a seqanswers.com discussion, Li Heng (lh3) says that PCR duplicates are usually identified after alignment, eg. by identifying read-pairs that have identical 5'-end coordinates.
Li Heng says that optical duplicates can be identified by checking the sequence and the coordinates on the image, and that alignment is not neeed to identify them.
Should we mark (and remove) duplicates from the analysis?
Li Heng says that marking (and removing duplicates) from your analysis is a good idea for SNP calling because you generally have high coverage data. However, he says it is dangerous to mark (and remove) duplicates for RNA-seq or ChIP-Seq where read count matters. He says it would be better to account for duplicates in your read counting model than run a duplicate-marking program.
Thanks to Bhavana Harsha for the link to Eric Vallabh Minikel's blog.
Monday, 5 August 2013
Clustering proteins using blastclust
A simple way to cluster proteins is using the blastclust program from NCBI. For example, if you have a fasta file of proteins, proteins.fa, you can cluster them by typing:
% blastclust -i proteins.fa -o proteins.fa.blastclust -p T -L .9 -b T -S 95
where '-o proteins.fa.blastclust' means the output file will be proteins.fa.blastclust; '-p T' means the proteins.fa file contains protein sequences; '-L .9 -S 95' means proteins are clustered together if they are >=95% identical over >=90% of their length; and '-b T' means that for two proteins A and B to be clustered, the length threshold must be reached with respect to both A and B.
The output file proteins.fa.blastclust contains one cluster per line, eg.:
NECAME_0000158501-mRNA-1 NECAME_0000508201-mRNA-1 NECAME_0000643601-mRNA-1 NECAME_0000812401-mRNA-1 NECAME_0001028301-mRNA-1 NECAME_0001537001-mRNA-1 NECAME_08585 NECAME_09673 NECAME_10885 NECAME_12595 NECAME_16785 NECAME_19488
NECAME_0000158401-mRNA-1 NECAME_0000508301-mRNA-1 NECAME_0000680701-mRNA-1 NECAME_08586 NECAME_09932 NECAME_16784
NECAME_0000680501-mRNA-1 NECAME_0001244101-mRNA-1 NECAME_00153 NECAME_09930 NECAME_18881
NECAME_0000012501-mRNA-1 NECAME_0000680601-mRNA-1 NECAME_00149 NECAME_00152 NECAME_09931
...
% blastclust -i proteins.fa -o proteins.fa.blastclust -p T -L .9 -b T -S 95
where '-o proteins.fa.blastclust' means the output file will be proteins.fa.blastclust; '-p T' means the proteins.fa file contains protein sequences; '-L .9 -S 95' means proteins are clustered together if they are >=95% identical over >=90% of their length; and '-b T' means that for two proteins A and B to be clustered, the length threshold must be reached with respect to both A and B.
The output file proteins.fa.blastclust contains one cluster per line, eg.:
NECAME_0000158501-mRNA-1 NECAME_0000508201-mRNA-1 NECAME_0000643601-mRNA-1 NECAME_0000812401-mRNA-1 NECAME_0001028301-mRNA-1 NECAME_0001537001-mRNA-1 NECAME_08585 NECAME_09673 NECAME_10885 NECAME_12595 NECAME_16785 NECAME_19488
NECAME_0000158401-mRNA-1 NECAME_0000508301-mRNA-1 NECAME_0000680701-mRNA-1 NECAME_08586 NECAME_09932 NECAME_16784
NECAME_0000680501-mRNA-1 NECAME_0001244101-mRNA-1 NECAME_00153 NECAME_09930 NECAME_18881
NECAME_0000012501-mRNA-1 NECAME_0000680601-mRNA-1 NECAME_00149 NECAME_00152 NECAME_09931
...
Friday, 2 August 2013
Magdalena's functional annotation pipeline
My colleague Magdalena
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog A"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog B"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51"
Run pfamscan to predict functions of proteins for which we don't have any functional prediction, or just prediction "hypothetical":
First make a fasta file of the proteins that don't have any functional prediction:
% perl -w ~alc/Documents/PerlScripts/mz3_annotation/getprotswithoutannotn.pl test.fa > test2.fa
[Note: at the moment this script doesn't take proteins marked 'hypothetical'].
Now run pfamscan using the protein fasta file as query, using Magdalena's script pfamscan_splitter.pl:
The output file 'functions2' looks like this:
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000357600.t1:mRNA /product="Pfam-B_3712 domain containing protein"
Magdalena said that the product chooser takes in several different functional annotations for a protein, and assigns a score to each alternative functional annotation. It tries to make the highest-scoring ones more similar to each other (eg. by changing lowercase to uppercase, changing word order, removing the last word, etc.).
Magdalena said that it if 3 of the functional annotations for a protein are 'hypothetical', and 7 say something different (and agree with each other), it will give the second annotation. However, if 7 of the annotations are 'hypothetical' and the other 3 all disagree with each other, the final annotation is 'hypothetical'.
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog A"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog B"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51"
Run pfamscan to predict functions of proteins for which we don't have any functional prediction, or just prediction "hypothetical":
First make a fasta file of the proteins that don't have any functional prediction:
% perl -w ~alc/Documents/PerlScripts/mz3_annotation/getprotswithoutannotn.pl test.fa > test2.fa
[Note: at the moment this script doesn't take proteins marked 'hypothetical'].
Now run pfamscan using the protein fasta file as query, using Magdalena's script pfamscan_splitter.pl:
The output file 'functions2' looks like this:
SRAE_2000311000.t1:mRNA /product=" DNA repair protein RAD51 homolog 1"
SRAE_2000357600.t1:mRNA /product="Pfam-B_3712 domain containing protein"
Magdalena said that the product chooser takes in several different functional annotations for a protein, and assigns a score to each alternative functional annotation. It tries to make the highest-scoring ones more similar to each other (eg. by changing lowercase to uppercase, changing word order, removing the last word, etc.).
Magdalena said that it if 3 of the functional annotations for a protein are 'hypothetical', and 7 say something different (and agree with each other), it will give the second annotation. However, if 7 of the annotations are 'hypothetical' and the other 3 all disagree with each other, the final annotation is 'hypothetical'.
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