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featurecounts of Rsubread strand specific orientation options

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
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updated by Carlo Yague Carlo Yague • written by ofonov • ofonov

1 answer

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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written by Carlo Yague Carlo Yague

Thanks for the link, it is helpful.

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written by ofonov • ofonov

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