MISO: Extraction of splicing events from user specified gene annotation (gtf or gff)

Question

[Anil Kesarwani]

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.

[xd_d]

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 ?

[Malcolm.Cook]

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?

[deshpandenandan1975]

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