The MACS software can be used to identify peaks in ChIP-Seq data. It can also be used for other similar data such as FAIRE-Seq data, although it was designed for ChIP-Seq data.
To run it, you type this:
% macs14 -t /nfs/users/nfs_s/sh23/ChIP_seq_data/Antib.sorted.bam -c /nfs/users/nfs_s/sh23/ChIP_seq_data/input_sorted.bam -f BAM -g 350000000 -n test-ChIP
where -t /nfs/users/nfs_s/sh23/ChIP_seq_data/Antib.sorted.bam specifies the ChIP-Seq data,
-c /nfs/users/nfs_s/sh23/ChIP_seq_data/input_sorted.bam specifies the control data,
-f BAM gives the format of the input files (BAM here),
-g 350000000 gives the effective genome size (350,000,000 for Schistosoma mansoni, as its genome is 350 Mb).
I submitted this job on the Sanger farm with 5 Gbyte of RAM.
An output file is made called test-ChIP_peaks.bed that has the positions of peaks identified.