Question: MISO: Extraction of splicing events from user specified gene annotation (gtf or gff)
1
gravatar for Anil Kesarwani
3.7 years ago by
United States
Anil Kesarwani90 wrote:

Hi, - MISO comes with its own set splicing events, which are used by MISO for event-specific PSI calculation. - For event-centric analysis, does MISO provide any tool for the extraction of splicing events from user specified gene annotation (gtf or gff) and prepare input for MISO. It would be extremely useful in picking events (novel) which are expressed in specific sample. Please advise me. Thanks.

rna-seq miso • 2.1k views
ADD COMMENTlink modified 2.3 years ago by deshpandenandan197520 • written 3.7 years ago by Anil Kesarwani90

I have the same Problem i found this https://github.com/yarden/rnaseqlib/blob/clip/rnaseqlib/gff/gff_make_annotation.py but it doesn't work.. Have someone an idea here ?

ADD REPLYlink written 3.7 years ago by xd_d110

Since that is the documented method for creating MISO compatible annotation, you might consider your problem to be to the yarden's code to work. What did you try? What happened?

ADD REPLYlink written 3.7 years ago by Malcolm.Cook1.1k

Hi all,

I have a related question.

I have a newly created novel.gff file from an annotated assembled transcriptome (which contains novel isoforms in addition to the Ensembl annotated ones).

How should I go about extracting splicing events from user specified gene annotation (novel.gff) and prepare input for MISO? Assuming that the above script does not work?

i.e. creating files such as

SE.mm9.gff RI.mm9.gff MXE.mm9.gff from my novel.gff file?

This will enable me to proceed to the next step index_gff --index SE.mm9.gff indexed/

regards,

Nandan

ADD REPLYlink written 2.3 years ago by deshpandenandan197520
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: 1644 users visited in the last hour
_