Dinh:COMPUTATIONAL/bisReadMapper

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Revision as of 01:45, 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.

# 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.