How STAR-fusion filter fusions?

[wei wu]

Dear all,

I am using STAR-Fusion to detect gene fusion in a cancer RNA-seq data. But I did not find any introduction file to explain how STAR-fusion do filter step no matter in wiki or the github webpage. Thus I want to ask what fusions have been filtered by STAR-fusion?

The filter steps I have found in that Nature Communication paper:

1. "the strands of the alignments were compared with the strands of the genes to keep only those consistent with a proper 5'-3' fusion"
2. "putative fusions between homologous genes were discarded; "
3. "putative fusions between genes and overlapping homologous genes were discarded as well"
4. filter fusions based on the number of chimeric reads and paired reads

Have the fiter steps descripted in the Nature Communication paper all done and what I need to filter in furthure analyses?

Besides, did STAR fusion filter fusions base on the distance between partners?

Can anybody answer my questoin or tell me the links about the introduction file which explains this but I ignored. Thanks!

Best wishes!
Wei

[Brian Haas]

STAR-Fusion uses this FusionFilter system:

  https://github.com/FusionFilter/FusionFilter/wiki

for filtering out likely false positives based on homology.  Other filters are up to users.  Also, the alignment settings in the STAR alignment will determine the minimum distance allowed between co-ordered gene pairs.  If reads are discordant, then the distance doesn't matter.

best,

~brian

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Brian J. Haas
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[wei wu]

Thanks Brian!

在 2016年10月20日星期四 UTC+8下午8:38:52，Brian Haas写道：

STAR-Fusion uses this FusionFilter system:

  https://github.com/FusionFilter/FusionFilter/wiki

for filtering out likely false positives based on homology.  Other filters are up to users.  Also, the alignment settings in the STAR alignment will determine the minimum distance allowed between co-ordered gene pairs.  If reads are discordant, then the distance doesn't matter.

best,

~brian

On Thu, Oct 20, 2016 at 3:26 AM, wei wu <weiws...@gmail.com> wrote:

Dear all,

I am using STAR-Fusion to detect gene fusion in a cancer RNA-seq data. But I did not find any introduction file to explain how STAR-fusion do filter step no matter in wiki or the github webpage. Thus I want to ask what fusions have been filtered by STAR-fusion?

The filter steps I have found in that Nature Communication paper:

1. "the strands of the alignments were compared with the strands of the genes to keep only those consistent with a proper 5'-3' fusion"
2. "putative fusions between homologous genes were discarded; "
3. "putative fusions between genes and overlapping homologous genes were discarded as well"
4. filter fusions based on the number of chimeric reads and paired reads

Have the fiter steps descripted in the Nature Communication paper all done and what I need to filter in furthure analyses?

Besides, did STAR fusion filter fusions base on the distance between partners?

Can anybody answer my questoin or tell me the links about the introduction file which explains this but I ignored. Thanks!

Best wishes!
Wei

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You received this message because you are subscribed to the Google Groups "STAR-Fusion" group.

To unsubscribe from this group and stop receiving emails from it, send an email to star-fusion...@googlegroups.com.

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To view this discussion on the web visit https://groups.google.com/d/msgid/star-fusion/7995932d-bf00-4796-8ff3-5879b2a757f7%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.