Dinh:COMPUTATIONAL/bisReadMapper

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Revision as of 02:07, 21 July 2012 by >Dinh
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To perform bisulfite reads mapping with bisReadMapper

Know where the following files and software are:

  1. Reference index
  2. soap or bowtie2
    currently I have bowtie2 running with --fast setting, which seems to be a lot slower than soap. this setting may be changed to --very-fast in the future for mapping BSPP data.
  1. samtools
  2. reads (do not need to copy the reads to the current directory, nor concatenate them)
  3. Methylation pipeline scripts (make sure you are either using the Triton version or the single-server version). The Triton version will make a number of job submissions!

Master shell script: 1 - perform mapping.

  • This master script process bisulfite reads.
  • Change this to use the correct reference genome. Either bisHg19 or bisMm9.
  • Change /home/ddiep/scripts to the correct path of the MethylationPipeline.
My_ref="/projects/zhang-lab/ddiep/bisHg19"
bisReadMapper="/home/ddiep/scripts/MethylationPipeline/bisReadMapper_Bowtie2.pl"
for f in list_*
do
        g=`echo $f | sed 's/list_//g'`
        /home/ddiep/scripts/MethylationPipeline/wBOWTIE/submitBSPPMapJobs.pl $g $My_ref $bisReadMapper < $f
done 
  • To run this master script, we need to be in the working directory and we need to create "list_SAMPLENAME" files. Each list file is simply a list of the location and names of all the reads files:
   For single end:
   /projects/zhang-lab/ddiep/TEST/s_6_1_Indx10.txt
   /projects/zhang-lab/ddiep/TEST/s_6_2_Indx10.txt
   For paired end:
   /projects/zhang-lab/ddiep/TEST/s_6_1_Indx10.txt /projects/zhang-lab/ddiep/TEST/s_6_2_Indx10.txt
  • Command to run:
sh Go.mapBisulfiteReads.sh

Master shell script: 2 - pull out methylation sites!

  • This master script process the mapped reads and call SNPs.
  • Again, make the necessary modifications so that it is specific to your genome: change reference path and change the list of chromosomes so that they are correct.
  • Again, make sure that the path to MethylationPipeline is correct.
My_ref="/home/ddiep/bisHg19"
for f in list_*
do
        g=`echo $f | sed 's/list_//g'`
        # human
        for c in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX chrY chrM
        # mouse
        #for c in chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chrX chrY chrM
        do
                /home/ddiep/scripts/MethylationPipeline/submitMergeAndExtractJobs.pl $g $c $My_ref 1
        done
done 
  • Command to run:
sh Go.mergeAndExtract.sh