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BAM Statistics


BAM Statistics takes as input an experiment definition holding bam files.

The BAM statistics accepts the following parameters in the option string:

  • 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;
  • isStranded=<true|false> wether the protocol was stranded
  • paired=<Null|paired|first|second> if reads are paired-end this parameter must be set otherwise the two ends will be counted twice, values are:
    • paired: combine the first and second read into pairs
    • first: use only the first read (this option can make sense if the second read is low quality)
    • second: use only the second read

  • keepUnpaired=<both|none|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
  • igvGenome=<genome name> the genome name to be sent to IGV, defaults to the build
  • gtf=<full path of gtf> if a gtf file should be used that is different from the default gtf in the build folder
  • gff=<full path of a gff> if a gff file should be used that is different from the default gtf in the build folder

Created by hubert. Last Modification: Wednesday November 14, 2012 11:13:28 CET by hubert.

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