[BioC] HTSeq-Count

[Julia [guest]]

Hi all,
I am new to the field of seq and performed a RIP-Seq experiment using HTSeq count as counter.
I get now the following (using union, but doesn´t look better for interesection_strict):
__no_feature	1503377
__ambiguous	490772
__too_low_aQual	0
__not_aligned	0
__alignment_not_unique	5277314
	
When I sum up counts for all genes, I get 3227845.

The number for __no_feature, __ambiguous, __alignment_not_unique look very high.

Does somebody have an idea for that?

(Additional info: We did random priming and mapped with STAR and masked rRNA loci)

Best wishes
Julia

 -- output of sessionInfo(): 

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