Dinh:COMPUTATIONAL/bisReadMapper
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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.