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Old 06-15-2011, 02:30 AM   #1
Location: Germany

Join Date: Sep 2009
Posts: 21
Default tophat fusion --fusion-min-dist


one more question about tophat fusion..
I run tophat fusion mit parameters tophat-fusion -o tophat_fusion -p 5 --allow-indels --no-coverage-search -r 0 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 /index/hg19 /runs_data/read1.fastq /runs_data/read2.fastq

The explanation for --fusion-min-dist in the manuel is For intra-chromosomal fusions, TopHat-Fusion tries to find fusions separated by at least this distance.
But I have in the fusions.out file a lot of lines like:
chr2-chr2 80917 80868 ff 1 1100 1 ....
As you see the distance between the fusion reads is only 49b.

what did I do wrong?

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Old 07-24-2011, 07:09 PM   #2
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Location: china

Join Date: May 2010
Posts: 9

Hi, MerFer

Your first site is larger than the second site, and the direction is ff, it means that the fusion is a downstream site fused with an upstream site.

Last edited by jiexiong; 07-24-2011 at 07:20 PM. Reason: I have pasted wrong words
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