hello,
I am running featureCounts on publicly available paired-end data. After alignment, I run featureCounts, but there are very few successfully assigned reads (only 25.2% successfully assigned).
I see
| Paired-end : no
Why is featureCounts not seeing that this data is paired-end? Is this why I am getting so few reads successfully assigned?
thanks.
I was confused by the menu option,
this made it sound like it automatically detects whether or not it is paired end.