Dinh:COMPUTATIONAL/bisReadMapper: Difference between revisions

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   3) samtools
   3) samtools
   4) reads (do not need to copy the reads to the current directory, nor concatenate them)
   4) reads (do not need to copy the reads to the current directory, nor concatenate them)
  5) Methylation pipeline scripts.
===Master shell script: 1 - perform mapping.===
===Master shell script: 1 - perform mapping.===
  <nowiki>
  <nowiki>
# This master script process bisulfite reads.
# 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"


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"
bisReadMapper="/home/ddiep/scripts/MethylationPipeline/bisReadMapper_Bowtie2.pl"



Revision as of 01:55, 21 July 2012

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)
 5) Methylation pipeline scripts.

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

# 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