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  • MerFer
    Member
    • Sep 2009
    • 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,
  • jiexiong
    Junior Member
    • May 2010
    • 9

    #2
    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, 07:20 PM. Reason: I have pasted wrong words

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