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Siva 03-08-2010 10:44 PM

Tophat and Bowtie Index
 
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.

thanks
Siva

Siva 03-09-2010 02:44 PM

Problem solved...Thanks Bill Spollen
 
Quote:

Originally Posted by Siva (Post 15103)
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.

thanks
Siva

Hi
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.

Thanks:)
Siva


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