I have ran STAR 2.5.0a on my bulk RNA-seq data, obtained using a single-end stranded library preparation strategy.
I have set --quantMode GeneCounts, to obtain the counts from the ''embedded'' htseq-count.
I have obtained results like the following:
N_unmapped 146273 146273 146273 N_multimapping 3408293 3408293 3408293 N_noFeature 355858 17068060 392326 N_ambiguous 1189135 11003 513338 ENSG00000223972 0 0 0 ENSG00000227232 2 0 2 ENSG0000027826 0 0 0 ENSG00000243485 1 1 0
Up to my knowledge:
the values in the second column represent the amount of hits that would have been obtained if the library prep. would have been not strand-specific (--stranded=no);
the third column contains the amount of hits that would have been obtained if the library prep. would have been strand specific with the ''stranded = yes'' setting;
the fourth column contains the amount of hits that would have been obtained if the library prep. would have been strand specific with the ''stranded = reverse'' setting.
Globally the results I have obtained call for a library preparation strategy consistent with the ''stranded = reverse'' setting, which is perfectly fine.
Inspecting the columns, what I would expect is that the values in the second column would represent the sum of the third and fourth columns, like this:
ENSG00000279457 17 0 17 ENSG00000248527 1260 1 1259
With the second entry calling for 1259 hits for the sense RNA and 1 hit for a possible asRNA
Anyways, I have also entries like the followings:
ENSG00000228794 126 0 129 ENSG00000187634 128 621 185 ENSG00000131584 205 15 205
How can I interpret such results ?