featureCount overlapping features from different strands

[haritz_irizar]

Hi all,

My name is Haritz Irizar and I am a postdoctoral fellow at the Icahn School of Medicine at Mount Sinai.

I'm intending to use featureCounts on single-end RNAseq data aligned with STAR to generate meta-feature-level counts using a .gtf file that combines Ensembl annotations and LNCipedia annotations for hg19.

The overlap between the lncRNA features and the Ensembl features is quite extensive and, while I want featureCounts to ignore the reads that map to overlapping features transcribed from the same strand, I'd like it to count in the reads that map to overlapping features transcribed from different strands.

Does any of you know how does featureCounts, if run without a -O flag, handle the reads that map to overlapping features transcribed from different strands? Does it count them in? Or, it ignores them as any other multi-overlapping read?

And, if the latter is true, any idea how could I tell featureCounts to count them in?

Thanks a lot for your help,

Haritz