Further to a previous PR (https://github.com/nunofonseca/irap/pull/88) submitted to address issues with exon-level quantification, this addresses the current lack of proper paired end handling when running featureCounts.
In order to count properly by fragment, the -p option needs to be passed for paired-end libraries. That is what this PR accomplishes.
Further to a previous PR (https://github.com/nunofonseca/irap/pull/88) submitted to address issues with exon-level quantification, this addresses the current lack of proper paired end handling when running featureCounts.
In order to count properly by fragment, the -p option needs to be passed for paired-end libraries. That is what this PR accomplishes.