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Old 03-09-2010, 01:44 PM   #2
Location: Ames, IA

Join Date: Nov 2008
Posts: 57
Smile Problem solved...Thanks Bill Spollen

Originally Posted by Siva View Post
Each time I run Tophat on a maize genome Bowtie index, I end up getting a bulky 2-4 GB reconstituted <*index.fa> file in my Tophat_out folder. I have tried to use this reconstituted index.fa file in my subsequent Tophat runs but it does not recognize this as a valid bowtie index file. Does Tophat always need the six <*.ebwt> files? Can I not substitute that with the single reconstituted <*index.fa> file from an earlier run? I want to save some disk space.

So if I copy the bulky <index.fa> file to the same folder that contains the six .ebwt files, this bulky file does not get written in the tophat_out folder every time. The manual makes a mention of this. Should have read carefully.

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