3.0 years ago by

Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia

You simply run featureCounts() with countMultiMappingReads=TRUE and fraction=TRUE.

The help page for featureCounts() says

"fraction:

logical indicating if fractional counts will be produced for multi-mapping reads. If TRUE, a fractional count, 1/n, will be generated for each reported alignment of a multi-mapping read, where n is the total number of alignments reported for that read. countMultiMappingReads must be set to TRUE when fraction is TRUE."

Both edgeR and limma accept fractional counts for analyzing RNA-seq data.

If you must round the counts, then rounding to the nearest integer (up or down) would be far better than rounding up. You can easily do this by:

fc <- featureCounts(files,countMultiMappingReads=TRUE,fraction=TRUE)
fc$counts[] <- round(fc$counts)

**Note**: fractional counting was introduced in Rsubread 1.20.0, so you must be using the latest release of R and Bioconductor.

Your R and/or Rsubread are probably old? Update them to the latest version and you should be able to see the 'fraction' argument.

2.9kI am using Rsubread_1.16.1 and updated all.

My R version is:

R version 3.1.2 (2014-10-31)

Platform: x86_64-unknown-linux-gnu (64-bit)

Still it is not working.

35k• written 3.0 years ago by tg369 •10The current version of R is 3.2.2 and the current version of Rsubread is 1.20.2.

Your software is two Bioconductor releases out of date, which is why it doesn't have the latest features.

You need to update to the latest versions of R and Bioconductor, as Wei already advised you.

35kMany thanks Gordon and Wei, that is working now after updating R version.

10Thank you very much Gordon.

However, I wonder why I am getting this error message:

Error in featureCounts(file = "co2a_STAR_gencodeAligned.out.sam", :

unused argument (fraction = TRUE)

Please could you advice me.

35k• written 3.0 years ago by tg369 •10