I'm trying to find the split reads that supported the fusion. I see in the results.tsv there is a column "splitr_count" showing how many split reads were present. In my case there are 9.
I also see a series of files named splitreads* within the output directory. When I grep for the ENSEMBL gene name within, say, splitreads.refseqs I only get back 2 lines. I've also tried grepping for the predicted junction sequence (found within *results.tsv) in splitreads.seq, which only returns 1 line.
What's the best way to get the split reads?
Thanks!
Last edit: eearley 2014-07-21
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Thanks for all your help in this forum!
I'm trying to find the split reads that supported the fusion. I see in the results.tsv there is a column "splitr_count" showing how many split reads were present. In my case there are 9.
I also see a series of files named splitreads* within the output directory. When I grep for the ENSEMBL gene name within, say, splitreads.refseqs I only get back 2 lines. I've also tried grepping for the predicted junction sequence (found within *results.tsv) in splitreads.seq, which only returns 1 line.
What's the best way to get the split reads?
Thanks!
Last edit: eearley 2014-07-21
Take a look at the README in the latest. Or just visit:
https://bitbucket.org/dranew/defuse
There is a section "Supporting Reads" which should tell you how to generate an output that may be helpful.
excellent. Thanks