Dinh:COMPUTATIONAL/bisReadMapper

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Revision as of 01:49, 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.
 3) samtools
 4) reads (do not need to copy the reads to the current directory, nor concatenate them)

Master shell script: 1 - perform mapping.

# This master script process bisulfite reads.

My_ref="/projects/zhang-lab/ddiep/bisHg19"
# Remember to use the correct number of nodes! Don't use too many nodes because this is slow
# Remember to set the correct temporary directory for sorting in this script!
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

# now we need to check that all jobs finished without error.

  • 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