Hello Folks,
I added an option to the SamTranscriptomeParser to reverse the strand of the 2nd read for paired end RNA-Seq so you don't have to delete it anymore when performing a stranded analysis. It also generates the sam header internally, exports unmapped reads, and gzips the output. See http://sourceforge.net/projects/useq/files/USeq_7.9.6.zip/download
-cheers, D
--
David Austin Nix, PhD
Huntsman Cancer Institute
Dept. OncSci University of Utah
Bioinformatics Shared Resource
HCI 3165 (801) 587-4611
dav...@hc...
Skype: NextGenBio
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