tag:blogger.com,1999:blog-7233518910685295571.post464667790795110072..comments2023-05-11T06:21:18.796-07:00Comments on avrilomics: LTRharvest and LTRdigestAvril Coghlanhttp://www.blogger.com/profile/14064447050845166903noreply@blogger.comBlogger9125tag:blogger.com,1999:blog-7233518910685295571.post-86724859075512243522017-12-21T01:42:23.249-08:002017-12-21T01:42:23.249-08:00Dear Agustin,
Sorry I don't know the answer to...Dear Agustin,<br />Sorry I don't know the answer to this. I'd recommend you email the developers of LTRharvest, I found them very helpful before.<br />Kind Regards,<br />AvrilAvril Coghlanhttps://www.blogger.com/profile/14064447050845166903noreply@blogger.comtag:blogger.com,1999:blog-7233518910685295571.post-74055101798285368432017-12-19T08:05:34.418-08:002017-12-19T08:05:34.418-08:00Hey Avril.
Im trying to run
gt -j 2 ltrdigest ...Hey Avril. <br /><br />Im trying to run <br /><br />gt -j 2 ltrdigest -pptlen 10 30 -pbsoffset 0 3 -trnas tRNA.fas -hmms HMM1.hmm -outfileprefix mygenome-ltrs ltrs ltrs_sorted.gff3 Muschr4.fsa <br /><br />but it gives me this ERROR<br /><br />gt ltrdigest: error: cannot guess file type of file tRNA.fas -- unknown file <br /><br /><br />Any idea how i can solve it? <br /><br /><br />Thx in advance,<br />Agustin<br /><br /><br /><br />ogi2487https://www.blogger.com/profile/02154423846693383021noreply@blogger.comtag:blogger.com,1999:blog-7233518910685295571.post-55406109572755927242015-12-04T09:30:52.270-08:002015-12-04T09:30:52.270-08:00Hey Avril!
That did it. Thanks so much for your h...Hey Avril!<br /><br />That did it. Thanks so much for your help. Your blog is a great resource!<br /><br />Best,<br />PeterAnonymoushttps://www.blogger.com/profile/08000053502619255213noreply@blogger.comtag:blogger.com,1999:blog-7233518910685295571.post-40279852660260602082015-12-03T01:05:38.471-08:002015-12-03T01:05:38.471-08:00Hi Peter,
Did you sort the gff output from ltrhar...Hi Peter,<br /><br />Did you sort the gff output from ltrharvest, ie.<br /><br />gt ltrharvest -index genome.fa -gff3 unsorted_input_gff<br /><br />gt gff3 -sort unsorted_input_gff > sorted_input_gff<br /><br />gt ltrdigest sorted_input_gff indexname > gff_result_file<br /><br />?<br />Regards,<br />AvrilAvril Coghlanhttps://www.blogger.com/profile/14064447050845166903noreply@blogger.comtag:blogger.com,1999:blog-7233518910685295571.post-51923825957369141202015-11-30T08:08:22.503-08:002015-11-30T08:08:22.503-08:00Hey Avril,
Yes, I have tried several iterations a...Hey Avril,<br /><br />Yes, I have tried several iterations and that is one of them. I get the same error for that and with the most basic ltrharvest command:<br /><br />gt ltrharvest -index pfof-aln6.fasta -gff3 pfoftest4.gff<br />gt ltrdigest -trnas pfoftest4.gff pfof-aln6.fasta<br />gt ltrdigest: error: cannot guess file type of file pfoftest4.gff -- unknown file contents<br /><br />I think there must be something wrong with the gff3 file that is being created. When I try to run gffread (a tool through cufflinks) I get this error:<br /><br />Peters-MacBook-Pro-2:documents pmh$ gffread pfoftest4.gff<br />Error parsing strand (?) from GFF line:<br />seq0 LTRharvest repeat_region 5669 10198 . ? . ID=repeat_region1<br /><br />Similarly, when I load the .gff file into Integrative Genomics Viewer it shows no elements, suggesting that it is having problems reading the file. I have reinstalled genometools and gotten the same error. If you have any thoughts please let me know, or I may try to run it on a different computer!<br /><br />Thanks,<br />Peter<br />Anonymoushttps://www.blogger.com/profile/08000053502619255213noreply@blogger.comtag:blogger.com,1999:blog-7233518910685295571.post-69637976266750255632015-11-30T00:49:22.338-08:002015-11-30T00:49:22.338-08:00Hi Peter,
Did you run ltrharvest like this:
gt ltr...Hi Peter,<br />Did you run ltrharvest like this:<br />gt ltrharvest -index genome.fa -seqids yes -tabout no > ltrharvest.out<br />?<br />Regards,<br />AvrilAvril Coghlanhttps://www.blogger.com/profile/14064447050845166903noreply@blogger.comtag:blogger.com,1999:blog-7233518910685295571.post-37499957311141684412015-11-29T23:00:42.647-08:002015-11-29T23:00:42.647-08:00Hey Avril!
Thanks so much for your post, it was ...Hey Avril! <br /><br />Thanks so much for your post, it was a great help. I wondered if you could help me with an issue I am having. It appears that ltrharvest is writing a gff3 file in a format that is not readable to ltrdigest. I get this error:<br /><br />Peters-MacBook-Pro-2:genometools-1.5.7 pmh$ gt ltrdigest -trnas pfoftest3.gff pfof-aln6.fasta<br />gt ltrdigest: error: cannot guess file type of file pfoftest3.gff -- unknown file contents<br /><br />Do you have any ideas for a solution? I've looked around and haven't seen similar posts.<br /><br />Thanks in advance,<br />PeterAnonymoushttps://www.blogger.com/profile/08000053502619255213noreply@blogger.comtag:blogger.com,1999:blog-7233518910685295571.post-64776092187033429572015-10-06T07:13:36.532-07:002015-10-06T07:13:36.532-07:00Dear Matthew,
Thanks for your comment.
I asked S...Dear Matthew,<br /><br />Thanks for your comment.<br /><br />I asked Sascha and he said that the '--' this is only important if the list of HMMs is the last option before the GFF and sequence files are given. <br />You don't need it if you had another option eg.<br />% gt ltrdigest -hmms file1.hmm file2.hmm file3.hmm -pdomevalcutoff 1e-5<br />name.fsa.gff3 name.fsa > outputfile<br /><br />He said it should be possible to use HMMER2 format HMMs, or HMMER3 format. If they are HMMER2 format, ltrdigest converts them to HMMER3 format itself (in /tmp directory).<br /><br />Thanks again!<br />Avril Coghlanhttps://www.blogger.com/profile/14064447050845166903noreply@blogger.comtag:blogger.com,1999:blog-7233518910685295571.post-37066532755020505352015-09-30T13:20:13.545-07:002015-09-30T13:20:13.545-07:00Hey, thanks for writing this post!
I love this so...Hey, thanks for writing this post!<br /><br />I love this software, but I had to leave a comment which is pretty important. When I was learning to use ltrdigest I discovered that some of the documentation is incorrect, but I forgot to contact anyone and you just reminded me now!<br /><br />Here's what I wrote in my lab notebook about it:<br /><br />It only took me like an hour and looking at the source code for ltrdigest to figure out that there is an undocumented flag that terminated the pHMMs, and also, they have to be in hmm3, unlike what the documentation says (it tells you you need hmm2).<br />Proper syntax is "gt ltrdigest -hmms list_of_hmms.hmm -- name.fsa.gff3 name.fsa > outputfile"<br /><br />I don't know if I needed HMM3 files because I had a newer version of hmmer, but I know I did :)<br /><br />Also, tell Sascha a huge thanks for having the source code available, since it allowed me to figure this out :)<br />Anonymoushttps://www.blogger.com/profile/11023285138874408207noreply@blogger.com