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itmat / Normalization

RNA-Seq normalization and quantification pipeline
https://github.com/itmat/normalization/wiki
GNU General Public License v3.0
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runall_head.pl needs flag for intergenic and intronic signal #11

Closed fossilfriend closed 10 years ago

fossilfriend commented 10 years ago

For my particular analysis, I am only interested in exonic signal, so don't need to run the mapping to introns or intergenic signal. I bypassed the intronic signal by setting -depthI to 0, but it would be nice to be able to have a flag to do the same for the intergenic signal.

eunjijunekim commented 10 years ago

i changed the script to only return exonmappers when -depthI is set to 0 and only return intron/intergenic mappers when -depthE is set to 0.