Dinh:COMPUTATIONAL/bisReadMapper
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How to perform bisulfite reads mapping with bisReadMapper
- Know where the following files and software are:
1) Reference index 2) soap 3) samtools 4) reads (do not need to copy the reads to the current directory, nor concatenate them)
- Write the parameters file:
Required: reads=s_5_1_sequence.txt,s_5_2_sequence.txt qualBase=[64/33] alignMode=[S/P] refDir=/path/to/bisRef soapDir=/path/to/soap samtoolsDir=/path/to/samtools soap2sam=/path/to/samtools/misc/soap2sam.pl name=Sample_Name (no space)
Optional: numCPU=[#], number of processors to use for mapping allC=[yes/no], calls all methylation in all contexts? rmdup=[yes/no], remove PCR duplicates using samtools rmdup? snp=/path/to/dbSNP/snp134.txt mapOnly=[yes/no], perform mapping only to generate sam files. trim5=[#], number of bases to trim from 5' trim3=[#], number of bases to trim from 3' qualTrim=[#], perform quality trimming using this quality score minDepth=[#], the minimum reads depth to call methylation in BED file.
- Run the software:
/path/to/bisReadMapper.pl sample_name.params
- To run the mapping on Triton, you need to write a *.job file!
#!/bin/csh #PBS -q small #PBS -l nodes=1:ppn=2 #PBS -l walltime=36:00:00 #PBS -o bisReadMapper_RL-KH4-Tn5mC_hg19.log #PBS -e bisReadMapper_RL-KH4-Tn5mC_hg19.err #PBS -V #PBS -M hdinhdp@gmail.com #PBS -m abe #PBS -A zhang-lab cd /projects/zhang-lab/ddiep/Working/WGBS_Rui_mm9/test_Hg19 /home/ddiep/softwares/bisReadMapper_v1.1/bisReadMapper.pl RL-KH4-Tn5mC.params
Note: - for each job file, modify the *.log and *.err file names to make it specific to the sample or run - wall time may needs to be increased for more reads. Longer walltime may put the job later in the queue, jobs with shorter walltimes will get processed faster. - change the email to your specific email address - change the "cd .. " to go to the current working directory - change the *.params file name, you can use the bisReadMapper in my directory.