I've looking for and answer on similar questions but i don't find what i suppose it's the problem. First I have 9 files of smallRNA-seq reads from human. I have aligned them with Bowtie2. I got a .sam file for each sample. Now I am counting with featureCounts. The results show 0% assigned reads for all the files. For alignment i use Ensemble human genome (GRCh38) My .gff3 file is from mirBase v22 (hsa.gff3) I used FeatureCounts with the following command:
featureCounts - t miRNA -g 'Name' -a /path/to/hsa.gff3 -o /path_to_all/*.sam
Similar Output for 9 samples:
|| Process SAM file sample_name.sam...
|| Single-end reads are included.
|| Total alignments : 58350348
|| Successfully assigned alignments : 26377 (0.0%)
|| Running time : 4.79 minutes