Dinh:COMPUTATIONAL/bisReadMapper: Difference between revisions
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== | ==To perform bisulfite reads mapping with bisReadMapper== | ||
# Know where the following files and software are: | # Know where the following files and software are: | ||
1) Reference index | 1) Reference index | ||
2) soap | 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 | 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) | ||
# 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. | ||
Revision as of 01:43, 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)
- 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.