View Single Post
Old 03-08-2010, 09:44 PM   #1
Siva
Member
 
Location: Ames, IA

Join Date: Nov 2008
Posts: 57
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 09:46 PM.
Siva is offline   Reply With Quote