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ed-lau / jcast

Junction centric alternative splicing translator
MIT License
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Is it possible to run jcast with splicing events that are not from rMATS ? #1

Closed gouthamatla closed 4 years ago

gouthamatla commented 4 years ago

Hi,

I am very interested to run jcast on few of my alternatively spliced transcripts, especially step 2 of the publication. I already have differentially used junctions, not from rMATS but from leafcutter, and I am curious to know the resulting protein sequences with usage of alternate junctions. Could you let me know if I could adapt it for this purpose ? Or is it possible to generate the spliced events from GTF using rMATs but without using BAM files ?

Thanks in advance, Goutham A

ed-lau commented 4 years ago

Hi Goutham,

jcast currently only takes in rMATS output rather than from leafcutter, although if there is enough interest we may go back and make it a more general purpose software in the future (accepting different workflows).

If you have the fastq or bam files it shouldn’t be too hard to re-run rMATS. As far as I know you will need more than GTF since rMATS has to count the junction specific reads. Hope that helps!

Best wishes, Edward

On Jan 9, 2020, at 9:07 AM, Goutham notifications@github.com wrote:

Hi,

I am very interested to run jcast on few of my alternatively spliced transcripts, especially step 2 of the publication. I already have differentially used junctions, not from rMATS but from leafcutter, and I am curious to know the resulting protein sequences with usage of alternate junctions. Could you let me know if I could adapt it for this purpose ? Or is it possible to generate the spliced events from GTF using rMATs but without using BAM files ?

Thanks in advance, Goutham A

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gouthamatla commented 4 years ago

Hi Edward,

Thanks for the quick response. I am not looking for differential splicing but just quantifying junctions and trying to asses the consequence of using alternate junctions in a single tissue especially junctions that are associated with genetic variants, like sQTL junctions.

Does jcast relies just on splicing events from rMATs or also on quantifications ? If I don't have two conditions or tissues, how would you suggest to run rMATs that can be fed in to jcast ?

Thanks, Goutham A