What Does Requirebothendsmapped From Rsubread Package Means?

Question

[roll]

Hi,

I am using the featureCounts from the Rsubread package. And I am trying to understand what does the requireBothEndsMapped option do. The manual says

"logical indicating if both ends from the same fragment are required to be successfully aligned before the fragment can be assigned to a feature or meta-feature. This parameter is only appliable when isPairedEnd is TRUE."

My data is paired end and i am counting miRNA,, so i provided miRNA as gtf and my bam file as my input.

Is this requireBothEndsMapped applicable in my case? Can you explain me in a simple way?

Answer 1

[dbpzdbpz]

Dear Roll,

Thank you for using featureCounts.

If you set "requireBothEndsMapped" to TRUE, featureCount ignores the read pairs (i.e., fragments) that have only one end mapped, but the other end unmapped. Generally speaking, requiring both ends to be mapped reduces sensitivity but improves specificity of read assignment.

Cheers,

Yang

[gaelgarcia]

Hi Yang,

I am trying to understand if the requireBothEndsMapped option will require both ends from a read pair to be aligned in general (regardless of which feature each end mapped to), or specifically to be mapped to the same feature / meta-feature?

Thanks for your help!

[Gordon Smyth]

The former, not the latter. The paired reads do not both have to overlap the same feature or meta-feature. In other words, the option does exactly what the documentation says and does not do anything extra that is not stated.