Question: featureCounts not recognizing paired-end alignment file.. why?
gravatar for dec986
2.1 years ago by
United States
dec986210 wrote:


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?


rna-seq featurecounts • 1.1k views
ADD COMMENTlink written 2.1 years ago by dec986210
gravatar for genomax
2.1 years ago by
United States
genomax78k wrote:

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.

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by genomax78k

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.

ADD REPLYlink written 2.1 years ago by dec986210
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1453 users visited in the last hour