I'm new to Bioinformatics. I need to write a pipeline for miRNA-Seq. The situation is the following: I have three normal samples and three cancer samples. I downloaded the stem-loop and the mature human sequences from miRBase, then I performed the mapping using Bowtie. Now I need to obtain the read counts for each sample; I'm trying to use featureCounts with mirBase hsa.gff3 file and my bam file but featureCounts doesn't work! It returns this:
Assigned 0 Unassigned_Unmapped 0 Unassigned_MappingQuality 0 Unassigned_Chimera 0 Unassigned_FragmentLength 0 Unassigned_Duplicate 0 Unassigned_MultiMapping 0 Unassigned_Secondary 0 Unassigned_Nonjunction 0 Unassigned_NoFeatures 1831739 Unassigned_Overlapping_Length 0 Unassigned_Ambiguity 0 This is my command: > featureCounts -t miRNA -g 'Name' -a my_path/hsa.gff3 -o my_path/my_bam_file
I have also tried with -g ID but the result is the same.
I have done a lot of researches but I don't understand where is the problem.