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bioinfoUGR / sRNAtoolbox

small RNA analysis programs: standalone jar files (sRNAbench, sRNAde, etc), manuals and Docker image
MIT License
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Any way to generate count matrix from web platform? #20

Open duz39 opened 1 year ago

duz39 commented 1 year ago

Hello! Thanks so much for making this resource publicly available. I was hoping to use the read counts generated by sRNAbench for differential expression analysis in separate software (tRNAs and RNAcentral output specifically), but I'm unable to find an output file with a full count matrix, and the "generate matrix" tool will only generate a read length matrix. I see that the ".grouped" files contain raw counts for each sample, but they're not in the same order between samples and they don't include the same annotations between files. Is there any way to obtain these data as a read count matrix? (or perhaps a way to transform the .grouped counts into a matrix?...apologies, I'm a novice in seq analysis). Thank you again!

bioinfoUGR commented 1 year ago

Thanks for your words, @duz39. For this you'd need to run a DE job using our tool from sRNAbench page. This will generate a summary count matrix. Download results as zip and you should find the matrix in there. If you include your jobID we may be able to help you further.