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Old 03-31-2010, 12:02 PM   #1
wenhuang
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Location: Raleigh, NC

Join Date: Feb 2010
Posts: 30
Default tophat -F/--min-isoform-fraction option

Hi,

I tried to discover novel junctions by tophat. One of the junctions it reported looked like this:

--In junctions.bed:
chr10 101101827 101102012 JUNC00036836 1 + 101101827 101102012 255,0,0 2 35,46 0,139

--On UCSC (see attached image):

My question is:

This appeared to be a false positive, though there were much lower coverage in the "intron" and the splice sites were canonical "GT-AG". There was only one alignment covering the junction (I checked the alignments by manually looking into this region of the SAM file).

Given the default -F/--min-isoform-fraction 0.15 and the high coverage in this region, should this junction not be considered? It seems like this is also an example of tophat looking into a single island for junctions as described in the tophat paper, otherwise the exon-exon junction would not be assembled in the first place.

Can someone explain a little bit how this --min-isoform-fraction work and why it is the case in my example?

By the way, is the 5th column in junctions.bed a coverage score?

Many thanks!
Attached Images
File Type: jpg hgt_genome_3df6_39a5a0.jpg (20.6 KB, 27 views)

Last edited by wenhuang; 03-31-2010 at 02:04 PM.
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