Dinh:COMPUTATIONAL/bisReadMapper: Difference between revisions

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(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==
=MOST CURRENT scripts: refer to the following wiki pages=
# Know where the following files and software are:
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2014/NOTES/2014-8-27] August 27, 2014.
  1) Reference index
[http://genome-tech.ucsd.edu/LabNotes/index.php/Dinh/Dinh_2013/NOTES/2013-1-7] January 7, 2013.
  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.

Latest revision as of 21:30, 27 August 2014

MOST CURRENT scripts: refer to the following wiki pages[edit]

[1] August 27, 2014. [2] January 7, 2013.