Hisat2 - combining several novel-splicesite-outfile lists from biological replicates ?
0
0
Entering edit mode
5.6 years ago

Hi all,

I'm doing a 2-pass mapping of RNAseq reads to an mm10 index using Hisat2 in a shell scripted loop. This question relates to combining several --novel-splicesite-outfile splice site lists from a bunch of biological replicate reads, to use as a single --novel-splicesite-infile for all the biological replicates in the 2nd pass.

So I've read somewhere that it is useful to combine several novel-splicesite-outfile files from the entire dataset during the first pass, remove duplicates, and use this expanded splicesite file as the --novel-splicesite-infile for the second pass for all replicates in the 2nd pass.

It's not stated lucidly (to me at least) in the manual, but I think this happens automatically when you feed a whole bunch of replicates into a single multi-read input in a hisat2 run, am I right?

best regards, K

RNA-Seq genome • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 1556 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6