Question: featurecounts of Rsubread strand specific orientation options
1
gravatar for ofonov
2.7 years ago by
ofonov10
ofonov10 wrote:

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?

Fragments
Fragment types

ADD COMMENTlink modified 2.7 years ago by Carlo Yague4.7k • written 2.7 years ago by ofonov10
2
gravatar for Carlo Yague
2.7 years ago by
Carlo Yague4.7k
Belgium
Carlo Yague4.7k wrote:

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)

enter image description here

Credit : Xianjun Dong

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Carlo Yague4.7k

Thanks for the link, it is helpful.

ADD REPLYlink written 2.7 years ago by ofonov10
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