How to get count matrix from aligned file

Question

[JulianC]

Hi everyone!

I'm working with microRNAs and I mapped my reads (from mirnaSeq) using the reference genome, so I obtained the BAM files of the alignment and also the BigWig. Now I have to do Differential Expression Analysis, but only considering miRNAs present in a particular region of the genome, so I would like to obtain a count matrix containing all miRNAs sequenced with the coordinates of the genomic regions and the number of reads for each one, in order to consider from them only the miRNAs I'm interested in. How can I do that starting from my alignments? Thank you for your help!

[h.mon]

I would like to obtain a count matrix containing all miRNAs sequenced with the coordinates of the genomic regions and the number of reads for each one, in order to consider from them only the miRNAs I'm interested in.

Don't do this, summarize and perform differential expression over all miRNAs. The analysis pipelines (edgeR, DESeq2, etc) uses information contained within the whole sample (depth of sequencing per sample, expression variance per treatment) to normalize counts and get better estimates of variation, in order to obtain more accurate results. You will be throwing away all this information, and possibly your results may reflect technical artifacts instead of true biological differences.