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gagneurlab / absplice

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Splicemap_tissues #27

Closed knakamura6222053 closed 8 months ago

knakamura6222053 commented 1 year ago

Dear Developer

Thank you for your making docker container.

I want to know about "Splicemap_tissues"

If I have a blood DNA sample but want to know the splicing mutations in the liver, can I select Splicemap_tissues for the liver?

neverov-am commented 1 year ago

Dear @knakamura6222053 ,

Thank you for your question and we are glad to hear that the container image solved your problem.

Yes, you can choose splicemap for liver working with a DNA sample from blood. You can choose your target tissue from the config file. The scores will show you the effect of the variants that you have in the DNA on splicing in your target tissue.

If you have additional RNA-seq from blood you could also run AbSplice-RNA on top of that. This will use the splicing measurement in blood and translate it to your target tissue (in your case liver).

knakamura6222053 commented 1 year ago

Thank you for Developer

I would like to detect more mitochondrial disease genes using Absplice.

In addition, I would like to ask one question. Can splicing abnormalities due to repetitive sequences be detected with this tool? For example, the repetitive sequences seen in Huntington's disease.

Various analyses using Absplice have given me new ideas, and I would like to have a meeting with you.

Best regards

WagnerNils commented 1 year ago

Dear @knakamura6222053, yes, we can have a meeting. I sent you an email to find a time slot.