Dinh:COMPUTATIONAL/bisReadMapper

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Revision as of 01:43, 21 July 2012 by >Dinh
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To perform bisulfite reads mapping with bisReadMapper

  1. 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)
  1. Master shell script: 1 - perform mapping.
 We need to perform mapping and make sure that all reads mapped properly.
  1. This master script process bisulfite reads.

My_ref="/projects/zhang-lab/ddiep/bisHg19"

  1. Remember to use the correct number of nodes! Don't use too many nodes because this is slow
  2. 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

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