Dinh:COMPUTATIONAL/bisReadMapper: Difference between revisions

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==To perform bisulfite reads mapping with bisReadMapper==
=MOST CURRENT scripts: refer to the following wiki pages=
===Know where the following files and software are:====
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2014/NOTES/2014-8-27] August 27, 2014.
  1) Reference index
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2013/NOTES/2013-1-7] January 7, 2013.
  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.===
<nowiki>
# 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.
</nowiki>
*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

Latest revision as of 21:30, 27 August 2014

MOST CURRENT scripts: refer to the following wiki pages[edit]

[1] August 27, 2014. [2] January 7, 2013.