htseq-count: reads with letter "N"

[zzhao2]

Hi,
I've just found that a read starting with letter "N" in my sam file was marked as "no_feature" by htseq-count. I hacked that read by changing the "N" to the reference letter and also modifying the affected fields such as FLAG and MD, and got htseq-count worked with that read. My question is: does htseq-count discard any reads with "N"s in anywhere, or just those starting with "N"s? It looks like that in that read all other letters of the sequence were same with the reference, so I would rather keep that read.
I raised this question because by using FastQC I've found that many of my reads have "N"s in their tails (3'?). Will htseq-count output better counts if I trim those tails?

Thanks,
Sylvia

[zzhao2]

Please ignore my initial post. The real reason why my read is not mapped is not the "N", it's because in the FLAG field it's marked as "0x10 SEQ being reverse complemented". When I change this single bit to 0, the read got counted. Does any body have any idea?