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
thanks
Siva
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