Hi, I have RNA-seq data (from ribodepleted samples) and i'm trying to map my reads to features using either htseq or featureCounts. The input for both is a bam file (reads were aligned using STAR) and a GTF file from ENSEMBLE. Both assign reads to exons by default.
FeatureCounts reported that ~33% of my reads were assigned to features, however when I'm trying to check how many reads were assigned using htseq, I saw that only 2% of my reads were assigned (There is no report in htseq so I summerized the second column in the results file, without the last 5 rows that contain the "no-feature" and "ambiguous" etc).
What is causing this difference between the two algorithms? Thank you very much!