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Old 01-05-2011, 09:51 AM   #1
Location: San Francisco

Join Date: Jul 2010
Posts: 10
Default junctions in tophat

When using TopHat v1.2.0, I am getting 5-fold more junctions identified when I give it an annotation file than when I do not give an annotation file.

12471 junctions - no annotation provided
58610 junctions - annotation provided, no novel junctions allowed
60048 junctions - annotation provided, novel junctions allowed

These are for 36 bp paired-end seqs from a mouse cell line.

Here's my (abbreviated) call with annotation:

tophat --GTF mm9.NCBIM37.59.fix.gtf --mate-inner-dist 104 --mate-std-dev 17 --solexa1.3-quals --segment-length 18 --keep-tmp --output-dir out mm9 left_sequence.txt right_sequence.txt &

Looks like TopHat has trouble finding junctions when it doesn't have annotation information. Has anyone else seen this? Thanks for input.
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