Hi all, I would like to know if it there was a Bioconductor package that could help me in the small RNAs quantifications. In particular I would use bam files as input and obtain a table with the read counts for each small RNA.
EDIT: It's not clear what you mean by 'small RNAs quantifications'. I suppose that could mean lots of different things. Assuming you mean something like 'I have some aligned data in bam files, and I want to count the number of reads that overlap just the small RNAs', then The conventional way to do that would be to use summarizeOverlaps from the GenomicAlignments package. You need a GRanges or GRangesList that identifies the genomic regions that the small RNAs come from, for which you can use an EnsDb package. Using the EnsDb.Hsapiens.v79 package as an example: