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Old 07-31-2010, 11:46 AM   #1
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Default Running Tophat with the GFF option


I am running Tophat with the --GFF option, where I supply it with the GFF of all the genes in my genome so that it can use those existing junctions in addition to discovering novel ones.

Two questions:

1. After the Tophat run, how can I check that Tophat actually used the junctions I gave it? Is there a .log file I can check? I cannot seem to find anything about the status of those junctions in "run.log".

2. Will Tophat make combinatorial use of the junctions I give it? In other words, if we have a gene with a single mRNA comprised of three exons, will it consider the junction where the middle exon is skipped, or does it only consider the junctions explicit in the GFF?

ethoswater is offline   Reply With Quote

alignment, bowtie, junctions, tophat

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