Dinh:COMPUTATIONAL/bisReadMapper: Difference between revisions
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qualTrim=[#], perform quality trimming using this quality score | qualTrim=[#], perform quality trimming using this quality score | ||
minDepth=[#], the minimum reads depth to call methylation in BED file. | minDepth=[#], the minimum reads depth to call methylation in BED file. | ||
bam=[yes/no], the input reads file are already mapped and sorted bam files. | |||
# | # To run the software anywhere: | ||
/path/to/bisReadMapper.pl sample_name.params | nohup /path/to/bisReadMapper.pl sample_name.params > sample_name.log & | ||
# To run the mapping on Triton, you need to write a *.job file! | # To run the mapping on Triton, you need to write a *.job file! | ||
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#PBS -m abe | #PBS -m abe | ||
#PBS -A zhang-lab | #PBS -A zhang-lab | ||
cd / | cd /phase1/ddiep/Working/WGBS_Rui_mm9/test_Hg19 | ||
/home/ddiep/softwares/bisReadMapper_v1.1/bisReadMapper.pl RL-KH4-Tn5mC.params | /home/ddiep/softwares/bisReadMapper_v1.1/bisReadMapper.pl RL-KH4-Tn5mC.params | ||
Note: | To submit the job: | ||
qsub name_of_file.job | |||
Note about running Triton job: | |||
- for each job file, modify the *.log and *.err file names to make it specific to the sample or run | - for each job file, modify the *.log and *.err file names to make it specific to the sample or run | ||
- wall time may needs to be increased for more reads. Longer walltime may put the job later in the queue, jobs with shorter walltimes will get processed faster. | - wall time may needs to be increased for more reads. Longer walltime may put the job later in the queue, jobs with shorter walltimes will get processed faster. | ||
- change the email to your specific email address | - change the email to your specific email address | ||
- change the "cd .. " to go to the current working directory | - change the "cd .. " to go to the current working directory. | ||
- change the *.params file name, you can use the bisReadMapper in my directory. | - change the *.params file name, you can use the bisReadMapper in my directory. | ||
- Since bisReadMapper generate a large amount of intermediate files, it is better to run on Oasis (ie. phase1/ddiep ) because it have a large storage capacity. Final methyl frequency files can be copied over to zhang-lab. | |||
- When calling all C methylation. I would run with "mapOnly=yes" in the parameters file. Post processing steps can be later be run in parallel on Triton. | |||
Post processing: | |||
(1) Convert sam to sorted bam (since samtools sort can't run in parallel, we will do this one at a time), but using just 1 node on Triton | |||
(2) Run multiple jobs of bisReadMapper with "bam=yes" in parallel for each chromosome. Note that each chromosome have a pair of *.bam files that is required for bisReadMapper |
Revision as of 19:58, 7 June 2012
How to perform bisulfite reads mapping with bisReadMapper
- Know where the following files and software are:
1) Reference index 2) soap 3) samtools 4) reads (do not need to copy the reads to the current directory, nor concatenate them)
- Write the parameters file:
Required: reads=s_5_1_sequence.txt,s_5_2_sequence.txt qualBase=[64/33] alignMode=[S/P] refDir=/path/to/bisRef soapDir=/path/to/soap samtoolsDir=/path/to/samtools soap2sam=/path/to/samtools/misc/soap2sam.pl name=Sample_Name (no space)
Optional: numCPU=[#], number of processors to use for mapping allC=[yes/no], calls all methylation in all contexts? rmdup=[yes/no], remove PCR duplicates using samtools rmdup? snp=/path/to/dbSNP/snp134.txt mapOnly=[yes/no], perform mapping only to generate sam files. trim5=[#], number of bases to trim from 5' trim3=[#], number of bases to trim from 3' qualTrim=[#], perform quality trimming using this quality score minDepth=[#], the minimum reads depth to call methylation in BED file. bam=[yes/no], the input reads file are already mapped and sorted bam files.
- To run the software anywhere:
nohup /path/to/bisReadMapper.pl sample_name.params > sample_name.log &
- To run the mapping on Triton, you need to write a *.job file!
#!/bin/csh #PBS -q small #PBS -l nodes=1:ppn=2 #PBS -l walltime=36:00:00 #PBS -o bisReadMapper_RL-KH4-Tn5mC_hg19.log #PBS -e bisReadMapper_RL-KH4-Tn5mC_hg19.err #PBS -V #PBS -M hdinhdp@gmail.com #PBS -m abe #PBS -A zhang-lab cd /phase1/ddiep/Working/WGBS_Rui_mm9/test_Hg19 /home/ddiep/softwares/bisReadMapper_v1.1/bisReadMapper.pl RL-KH4-Tn5mC.params
To submit the job: qsub name_of_file.job
Note about running Triton job:
- for each job file, modify the *.log and *.err file names to make it specific to the sample or run - wall time may needs to be increased for more reads. Longer walltime may put the job later in the queue, jobs with shorter walltimes will get processed faster. - change the email to your specific email address - change the "cd .. " to go to the current working directory. - change the *.params file name, you can use the bisReadMapper in my directory. - Since bisReadMapper generate a large amount of intermediate files, it is better to run on Oasis (ie. phase1/ddiep ) because it have a large storage capacity. Final methyl frequency files can be copied over to zhang-lab. - When calling all C methylation. I would run with "mapOnly=yes" in the parameters file. Post processing steps can be later be run in parallel on Triton. Post processing: (1) Convert sam to sorted bam (since samtools sort can't run in parallel, we will do this one at a time), but using just 1 node on Triton (2) Run multiple jobs of bisReadMapper with "bam=yes" in parallel for each chromosome. Note that each chromosome have a pair of *.bam files that is required for bisReadMapper