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williamritchie / IRFinder

Detecting intron retention from RNA-Seq experiments
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Column header for IRFinder-IR-nondir.txt #43

Closed lpantano closed 6 years ago

lpantano commented 6 years ago

Hi!

thanks for creating and maintaining this tool!

I tried to find the headers for this file, but I couldn't find it.

I want to run IRfinder for just a couple of samples to know the intron retention percentage for some transcripts but I don't want to do differential expression analysis. Can you help me to know which file and value should I check on just to look at a metric that would tell me that for individual samples?

Thanks a lot!

dg520 commented 6 years ago

Hi @lpantano ,

If your RNA libraries are non-directional, IRFinder-IR-nondir.txt is the file you're looking for. Otherwise, it's IRFinder-IR-dir.txt. A detailed description of file header can be found at: https://github.com/williamritchie/IRFinder/wiki/About-Main-Output-File

The 20th column (second last) is IR ratio you're interested in. I also recommend you to check column 19 (number of reads supporting the correct splicing of the junction) and column 8 (how much percentage of the entire intron length is covered by reads). For conservation, you might also wanna filter based on the warning information (e.g. only keep rows with "-" or "NonUniformIntronCover" in the last column).

Best, Dadi

lpantano commented 6 years ago

Thanks! this is awesome!