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Old 03-08-2010, 10:44 PM   #1
Siva
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Location: Ames, IA

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Unhappy 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

Last edited by Siva; 03-08-2010 at 10:46 PM.
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Old 03-09-2010, 02:44 PM   #2
Siva
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Smile Problem solved...Thanks Bill Spollen

Quote:
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.

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.

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Siva
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