Dinh:COMPUTATIONAL/bisReadMapper

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Revision as of 19:12, 7 June 2012 by >Dinh (Created page with "==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 no...")
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How to perform bisulfite reads mapping with bisReadMapper

  1. 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)
  1. 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.