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Old 06-20-2013, 05:08 AM   #1
EGrassi
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Location: Turin, Italy

Join Date: Oct 2010
Posts: 66
Default tophat 2.0.0 and index fasta file

Hello, I was wondering, as long as I believe that bowtie only uses its indexes to perform
the alignments, what does tophat do with the reference fasta file referred here:
Quote:
TopHat also requires a fasta file (.fa) for your reference. If this file is not found alongside the other index files, the program will use the Bowtie index you give it to build this file and save it to the output directory. This step can take up to an hour for a human-sized genome. To skip this step in future runs, you can move the fasta file from the tophat_out directory to the directory containing the Bowtie index files.
(http://tophat.cbcb.umd.edu/tutorial.shtml).

I am asking this because in my lab we erroneously used indexes without the random chr (from UCSC) but an index fasta file that has them. The resulting bam is different from the one derived with the "rebuild by tophat" fasta and therefore we will realign all the affected files but I would like to understand what's happening inside tophat (hopefully without scavening in the python wrapper and in a tons of C++ tools that have that fasta as an argument in run.log).

Thanks,
E.
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