Count BAM


Compute expression taking BAM files as input. Expression estimates are computed for transcripts!

Available methods are:

  • countBamHits: count for each transcript the overlapping read (read pairs if paired-end sequencing);
  • countCufflinks: use Cufflinks to do expression estimation (coming soon)
  • countRsem: use RSEM to do expression estimation (coming soon)
  • countMmseq: use MMSEQ to do expression estimation (coming soon)
  • countHTSeq: use HT-seq to get counts

B-Fabric provides the following options:
  • Name: a suffix that will appended to the file name
  • Method: one of the methods above
  • build: 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
  • isStranded
  • transcriptClass: use "genes" to use the genes.gtf found in the reference specified by the build
  • paired
  • Options:
    • featureLevel=<exon|intron|transcript|tss|gene> (only used by countBamHits>
    • minFeatureOverlap=<min number of bases of the read overlap> (only used by countBamHits>
    • 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:
      • gtf=<full path to gtf file to be used>
    • keepUnpaired=<none|both|first|second> in the case of paired-end whether also consider reads that are only half-mapped
    • useChr=<chromosome name list> use only the chromosomes in the comma-separated list