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Xinglab / rmats-turbo

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number of depth for a common sample are different. #426

Closed mbk0asis closed 3 months ago

mbk0asis commented 3 months ago

Hi, I have two sets of splicing events at two mutation sites. For comparison, I used a single WT sample (blue) as a control in both cases, but the read depth for WT are different. Since coordinates shown in the plots are identical, I think the read depths also should be the same. Would you explain why they have different number of reads?

image

EricKutschera commented 3 months ago

It might be that the two events have slightly different coordinates and the 885 junction and the 821 junction are different junctions. What rmats2sashimiplot commands did you run? If you run with the -c argument and not the -e argument then it should plot all the junctions in the region: https://github.com/Xinglab/rmats2sashimiplot/tree/v3.0.0?tab=readme-ov-file#bam-files-with-coordinate-and-annotation

mbk0asis commented 3 months ago

Thank you for the explanation! After checking the coordinates, I found the first one covered more region. I will close this issue. Thank you again!!!