Dinh:COMPUTATIONAL/bisReadMapper: Difference between revisions

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   We need to perform mapping and make sure that all reads mapped properly.
   We need to perform mapping and make sure that all reads mapped properly.


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# This master script process bisulfite reads.
# This master script process bisulfite reads.



Revision as of 01:45, 21 July 2012

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.