Question: Hisat2 - combining several novel-splicesite-outfile lists from biological replicates ?
0
gravatar for kieran.short
2.1 years ago by
kieran.short0 wrote:

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 • 516 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by kieran.short0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1571 users visited in the last hour