I made some changes to the cufflinks and tophat wrapper to pull gtf files from 
an indexed loc file as  opposed to from history. The diff's are attached. I 
made it an optional feature. Please let me know if this makes its way into 



Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.com<mailto:icho...@illumina.com>
Website: www.illumina.com<http://www.illumina.com>

Attachment: cufflinks_wrapper.xml.diff
Description: cufflinks_wrapper.xml.diff

Attachment: tophat_wrapper.xml.diff
Description: tophat_wrapper.xml.diff

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