featurecounts of Rsubread strand specific orientation options
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4.7 years ago
ofonov ▴ 10

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

Rsubread featurecounts strand specific • 2.3k views
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4.7 years ago

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

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Thanks for the link, it is helpful.

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