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How to locate the difference in splicing units to transcripts or isoforms? #148

Open Yichel518 opened 3 years ago

Yichel518 commented 3 years ago

Hello, I am an avid user of the rMATS tool and have found many splicing sites and events. Now I have obtained alternative spling events of the differences between the two groups of data. For example, SE, I have obtained the results of SE event units, but I would like to locate these events to specific transcripts or isoforms, and I would like your advice to help me! Thanks!

EricKutschera commented 3 years ago

For a particluar SE event in the SE.MATS.JC.txt output file, you can see the coordinates for the exons in the columns: chr, strand, (exonStart_0base, exonEnd), (upstreamES, upstreamEE), (downstreamES, downstreamEE)

I have a script that uses those coordinates to find matching transcripts in the GTF file. Maybe you can modify that script to find what you are looking for se_to_isoforms.zip

Yichel518 commented 3 years ago

thank you for your attention and help! I would study your methods to find matching transcripts. thank you again!

Yichel518 commented 3 years ago

When I use the se_to_isoforms.py script you provided, CHR, Strand, (exonStart_0base, exonEnd), (upstreamES, upstreamEE), (downstreamES, downstreamEE) information I print in but no result displayed, I don't know what happened, Have you ever come across a similar situation?

EricKutschera commented 3 years ago

I would expect that script to find at least 1 transcript if you copied the coordinates directly from the SE.MATS output file and used the same gtf that was used to run rmats. Can you post the command line you used?

Did you use --novelSS when running rmats? I think the script may not work for events in fromGTF.novelSpliceSite.SE.txt

joeellis1331 commented 3 years ago

For a particluar SE event in the SE.MATS.JC.txt output file, you can see the coordinates for the exons in the columns: chr, strand, (exonStart_0base, exonEnd), (upstreamES, upstreamEE), (downstreamES, downstreamEE)

I have a script that uses those coordinates to find matching transcripts in the GTF file. Maybe you can modify that script to find what you are looking for se_to_isoforms.zip

It would be great to integrate this into the output format of rMATS. I, as well as many other peers, look for this information!

EricKutschera commented 3 years ago

Thanks for your suggestion. The existing script is for finding isoforms for an individual event. More work would be needed to include isoform information for all the events in the rMATS output. We may add that feature sometime in the future, but it's not something I'm planning to implement soon

Yichel518 commented 3 years ago

Thank you for your discussion and suggestions. I will use this script after I modify it. Thank you for your selfless help again!