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gagneurlab / splicemap

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Access to XXXX_raw_count_table.csv #2

Open shiro-kur opened 1 year ago

shiro-kur commented 1 year ago

Hi,

How can I access XXXX_raw_count_table.csv ?? The File is manipulated in the example.ipynb. The splicemap_download command appears to download only psi files (e.g. XXXX_splicemap_psi5_method=kn_event_filter=median_cutoff.csv.gz).

I felt the the raw_count_tables are also very valuable.

WagnerNils commented 1 year ago

Hi, the raw split-read counts are provided by FRASER. We use them in our tool AbSplice-RNA to infer changes in psi in non-accessible tissues from RNA-seq measurements of an accessible tissue. Have a look at the example use case of AbSplice-RNA in the absplice repo. In the provided workflow we save the raw count tables with this script to this file and use them to infer changes in psi.