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Count Reads


Directly compute expression taking read files (e.g. .fastq) as input. Expression estimates are computed for transcripts!

Available methods are:

  • countRsem: use RSEM to do expression estimation
  • countCufflinks: use Cufflinks to do expression estimation
  • countMmseq: use MMSEQ to do expression estimation


B-Fabric provides the following options:
  • Name: a suffix that will appended to the file name
  • Method: one of the methods above
  • Options:
    • trimleft=N : number of bases to trim from the left end
    • trimRight=N : number of bases to trim from the right end
    • nReads=N : number of reads to use; helpful for making a quick test run on, e.g. only 1Mio reads
    • doPairReads=true|false : default true, i.e. if R1 reads are provided, and there are R2 reads, then both will be used and paired mapping will be done; pairing assumes the forward-reverse orientation of the two reads (corresponding to the --fr option in Bowtie)
    • build=<build name> : the name of a genome build in our reference folder /srv/GT/reference to use; the script will find the default genome sequence and gtf file for the build; if a mapper needs an index, the index is generated automatically and placed in the reference folder
    • additionally if the references are not in the reference directory or if a custom reference should be used the references can be set explicitly by specifying:
      • ref=<full path to reference genome index to be used>
      • gtf=<full path to gtf file to be used>
    • everything else that is in the option field will be passed as is to the respective application (RSEM, cufflinks, MMSEQ)


Created by hubert. Last Modification: Wednesday July 18, 2012 13:54:43 CEST by hubert.

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