IGB User's Guide
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changes.mady.by.user Nowlan Freese

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changes.mady.by.user Paige Kulzer

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Comment: Removed the word "Optional" from the -u flag in the last section of this page to be more consistent with the rest of the flags.

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  • -u (unique) Ensures that only uniquely mapping spliced reads (with NH tag equal to 1) will be used to construct junctions. Default is to use all reads regardless of mapping quality or number of mappings obtained. Optional.
  • -n Number of bases that must map to either side of a putative intron for a spliced read to be used to create or support a junction feature. Default is 5.
  • -b Absolute path to a .2bit format genomic sequence file that will be used to identify junction strand. Required.
  • -o (output) Name of the junctions file that will be written. Default is print to stdout.

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