"__no_feature " read in SAMPLE_ID.transcript_counts.tsv file

[SweetGojoSatoru]

Thanks for developing this nice tool.I have met a problem, how should I interpret the meaning of the "__no_feature" read statistics in the last three lines of the SAMPLE_ID.transcript_counts.tsv file?

$ tail -n 5 OUT.gene_counts.tsv
ENSMUSG00000095019 0.00
ENSMUSG00000095041 10.00
__ambiguous 298
__no_feature 719891
__not_aligned 0

[andrewprzh]

Dear @SweetGojoSatoru

Thanks for the feedback!

As far as I remenber, these lines are derived from a popular short-read tool featureCounts.
__no_feature represents the number of reads that were not assigned to any gene/isoforms, i.e. most likely due to being mapped to intergeneic/intronic space.

Best
Andrey