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I am attempting to use Tophat to analyze some data for our lab, and have fun into a snag. I have downloaded a pre-built index from the Tophat/Bowtie website, which contains various .ebwt files. However, upon running tophat, I get the error that Tophat needs a .bfa file. I'm not sure why it requires a .bfa file, but, in another data set, I have a fasta file, and upon changing the name form '.fa' to '.bfa', Tophat works.
I read the Tophat website, and it claims that Tophat can assemble a fasta file (.fa) if I don't have one, but whenever I try to run Tophat, it never states that it can assemble this file. The only response I get is that Tophat needs a '.bfa' file.
Any ideas what I might be doing wrong to prevent Tophat from assembling this .bfa file, or is there another method you'd suggest I use to make a fasta file on my own?
I read the Tophat website, and it claims that Tophat can assemble a fasta file (.fa) if I don't have one, but whenever I try to run Tophat, it never states that it can assemble this file. The only response I get is that Tophat needs a '.bfa' file.
Any ideas what I might be doing wrong to prevent Tophat from assembling this .bfa file, or is there another method you'd suggest I use to make a fasta file on my own?