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gagneurlab / absplice

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How to get CATs data #26

Closed Eyulaochen closed 2 days ago

Eyulaochen commented 1 year ago

I want to get CATs data to validate the absplice performance. How to get CATs data?

WagnerNils commented 1 year ago

I am not sure if I understand your question. So here I just give you some general information. Let me know if you need something specific. CAT is short for clinically accessible tissue (like blood or skin). We use this extra information in AbSplice-RNA. The idea is that we have DNA and RNA information of the same individual available. From the RNA measurements we can then infer splicing changes in non-accessible tissues (like brain or heart) using outlier calls in the CAT and SpliceMap information of both the accessible and non-accessible tissue to translate the variant effects to the non-accessible tissue. You need the RNA-seq data from an individual in order to run AbSplice-RNA. Patient data is private information and can not be shared; so we used dummy data in our AbSplice-RNA example.

Let me know if you need further assistance

Eyulaochen commented 1 year ago

AbSplice-RNA don't need tissue specific?

Sokhanetaze80 commented 1 year ago

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WagnerNils commented 1 year ago

Dear Eyulaochen, again I am not sure if I understand your question; can you be more specific of what you are trying to accomplish?

With AbSplice-RNA you can predict in any target tissue that you have a SpliceMap from and that you define in the field splicemap_tissues in the config file. In that sense it is the same as AbSplice-DNA. The difference in AbSplice-RNA is that you additionally provide RNA-seq information of an accessible tissue (e.g. blood or fibroblasts). The idea is that we can measure the variant effect directly in the accessible tissue; if splicing is similar in the accessible tissue and the target tissue (which we know from our SpliceMaps) we can predict that the variant effect will lead to a splicing outlier in the target tissue if we measured a splicing outlier in the accessible tissue.

Eyulaochen commented 1 year ago

Sorry for asking stupid questions. Let me read the article carefully. Appreciate your help!

WagnerNils commented 1 year ago

No worries; your questions were not stupid. I was just not sure if my general answers were what you wanted to know and would otherwise need a little bit more context to give you a more specific answer. Let me know if something is still unclear and if you need more help.

Eyulaochen commented 1 year ago

Dear Dr. Wagner, I see. Really appreciate your help! Best regards, Huayang