I used htseq-count http://www-huber.embl.de/users/anders/HTSeq/doc/count.html to count the pair-end RNA-seq data.
at the end, there are warnings like
Warning: 8612298 reads with missing mate encountered.
my question is how htseq-count deals with the pairs with only one end existing in the sam file?
does htseq-count simply discard those counts?