runall_head.pl needs flag for unique/non-unique mappers

itmat / Normalization

RNA-Seq normalization and quantification pipeline

https://github.com/itmat/normalization/wiki

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runall_head.pl needs flag for unique/non-unique mappers #10

Closed fossilfriend closed 10 years ago

fossilfriend commented 10 years ago

Prior to running runallhead.pl I've run relevant scripts with the -u option to deal with only unique mappers. However, no such flag exists for the script runall_head.pl, which dies looking for the non-existent non-unique exonmappers sam files, with the following message:

ERROR: The file '/READS//NU/.filtered_nu_exonmappers.1.sam' does not seem to exist...

eunjijunekim commented 10 years ago

i added -u and -nu options to the script.