featureCounts -- Features and meta-features

[kaiyang zhang]

Hi,

I was using featureCounts to count a set of short single-end reads, and there were more reads assigned when it was performed at meta-feature level (genes) than at feature level (exons). I am wondering if the meta-feature is a set of features (in this case just count exonic hits) or it is a range of positions (also including intronic hits)?

Thanks in advance for your help.

Kaiyang

[Wei Shi]

Hi Kaiyang,

Could you provide your commands for gene-level and exon-level counting? The parameters used in your commands affect how many reads are counted.

Mata-features are always the set of features, so for summarizing RNA-seq reads to genes or exons each gene includes a set of exons and it does not include intron regions.

Best wishes,
Wei