tophat fusion --fusion-min-dist

[MerFer]

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]

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.