Expression Counts from Bam Files of miRNA-seq data

Question

[tfo]

Hello,

I am new to bioinformatics. I have been given bam files (aligned to a reference genome) of miRNA-seq data. My goal at this moment is to retrieve miRNA expression counts. The bam files are only labeled with the chromosome locus for each miRNA, not the miRNA names themselves, making it seemingly impossible to retrieve miRNA counts.

Does anyone have any suggestions for how to approach this problem? I feel very stuck and lost.

Answer 1

[swbarnes2]

Look up a program called featureCounts, part of the subread software package. Then you need a gtf or gff with miRNA coordinates.

[tfo]

I will try featureCounts, thank you for your help!