featureCounts not recognizing paired-end alignment file.. why?

Question

[dec986]

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.

Answer 1

[GenoMax]

Are you adding -p option to signify that you want fragments counted (not reads, in case of PE)? Just to be sure the alignment was done using PE reads at the same time, correct?

Also remember that multi-mapping reads are not counted by default so that may explain the low % of assignment.

[dec986]

I was confused by the menu option,

-p                  If specified, fragments (or templates) will be counted
                      instead of reads. This option is only applicable for
                      paired-end reads.

this made it sound like it automatically detects whether or not it is paired end.