Dinh:COMPUTATIONAL/bisReadMapper
Jump to navigation
Jump to search
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)
Master shell script: 1 - perform mapping.
# 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.
- 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