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ChristopherWilks / snaptron

fast webservices based query tool for large sets of genomic features
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Inquire the intron junctions of srav2 #18

Closed tewengtong closed 4 months ago

tewengtong commented 1 year ago

Hi, I'm recently using snaptron for my analysis. I saw there is a column called "DataSource:Type" （https://snaptron.cs.jhu.edu/srav2/snaptron?regions=ABCD3）, but I could find it in the srav2-junction files (https://snaptron.cs.jhu.edu/data/srav2/junctions.bgz). Would please tell me how can I extract all the intron junctions from sra2 dataset? Or how to get this column? Thank you very much!

ChristopherWilks commented 1 year ago

Hi @tewengtong,

The Snaptron (the service) adds the prefix of the compilation to each row on return (e.g. in this case "srav2"). That said, the backing data file, https://snaptron.cs.jhu.edu/data/srav2/junctions.bgz only contains junctions from the srav2 compilation, so any/all junctions there are what you're looking for if you're only interested in srav2 junctions.