when using htseq-count, should I only count read-pairs whose two mates were both reported ?
Hi all:
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!
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1 answer
I prefer to count orphans as well. Sometimes one of the reads just has crap quality and doesn't align, I see no reason to deflate counts because of that.
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Devon Ryan
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