featureCount how to count reads on either + or - strand

Question

[coral90]

Hi,

I know this is a bit unusual question. But here it is. I have small RNA sequencing data. Say, I have a gene on + strand as indicated in the gtf file. However, I would like to know the reads that align to both + and - strand of the genome. How can I set the parameter to achieve this? Thanks!

Xinlian

Answer 1

[h.mon]

If you just issue featureCounts without arguments on the command-line, you would be given a full list of parameters. Reading then, you would find:

  -s <int>            Perform strand-specific read counting. Acceptable values:
                      0 (unstranded), 1 (stranded) and 2 (reversely stranded).
                      0 by default.