featurecounts of Rsubread strand specific orientation options

Question

[ofonov]

Hi,

Featurecounts of Rsubread package has two options for stranded libraries: 1 (stranded) and 2 (reversely stranded). What is the difference between these two? How the reads should be orientated, which option on the attached picture corresponds to stranded and to reversely stranded?

Fragment types

Answer 1

[Carlo Yague]

Stranded and reversely stranded match the A on your picture. check this blog post for more insight :

A_2 = fr-firststrand = reversely stranded (the R2 read is in the same direction than the RNA fragment)

A_1 = fr-secondstrand = stranded (the R1 read is in the same direction than the RNA fragment)

Credit : Xianjun Dong

[ofonov]

Thanks for the link, it is helpful.