Working with pair-end RNA-seq data,
I found that for some read-pairs, only one end/mate was reported by tophat-output sam file and then htseq-count.
For such cases, what would you do in usual when calculating gene-wise read count ?
( I think I should only count those read-pairs whose both ends were successfully aligned and reported by htseq-count. )
Your opinions must be very valuable.
Thanks in advance!