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Forum: Bioinformatics 04-23-2010, 10:07 AM
Replies: 10
Views: 9,270
Posted By thinkRNA
Now that I read the tophat parameters in detail,...

Now that I read the tophat parameters in detail, there is a lot of tailoring one can do to align low abundance reads. Especially, look at this one:

-F/--min-isoform-fraction <0.0-1.0> TopHat...
Forum: Bioinformatics 04-23-2010, 09:51 AM
Replies: 10
Views: 9,270
Posted By thinkRNA
Tophat will only align your reads to the...

Tophat will only align your reads to the junctions you provide. As you mention, you can definitely increase coverage by providing your own more comprehensive GFF file or if you can read this post...
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