Running Tophat with the GFF option

ethoswater · 07-31-2010, 11:46 AM

Hello,

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?

Thanks.

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07-31-2010, 11:46 AM	#1
ethoswater Junior Member Location: USA Join Date: Jul 2010 Posts: 2	Running Tophat with the GFF option Hello, 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? Thanks.