tophat fusion --fusion-min-dist

MerFer · 06-15-2011, 02:30 AM

Hello,

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?

Thanks,

jiexiong · 07-24-2011, 07:09 PM

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.

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06-15-2011, 02:30 AM	#1
MerFer Member Location: Germany Join Date: Sep 2009 Posts: 21	tophat fusion --fusion-min-dist Hello, 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? Thanks,

07-24-2011, 07:09 PM	#2
jiexiong Junior Member 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