Question

ribosomeProfilingQC - countReads function - is it possible to consider library type - non-stranded, forward-stranded or rev-stransded?

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alexandr.gopanenko ▴ 50

@alexandrgopanenko-11598

Last seen 17 months ago

Germany

Hi!

I want to calculate RPFs for my Ribo-seq experiments using countReads function from ribosomeProfilingQC. The question: is there any way to take into consideration library type (non-stranded, forward-stranded or rev-stranded and PE or SE)? Like it possible to do, for instance, using featureCounts from Rsubread...

Unfortunately, I didn't find that information in the reference manual.

Thanks in advance,

Best regards,

Alexandr

ribosomeProfilingQC countReads • 1.2k views

ADD COMMENT • link 3.8 years ago alexandr.gopanenko ▴ 50

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Hi Alexandr,

Sorry I missed this message. Thank you for trying ribosomeProfilingQC. Yes, that is a great idea to expose arguments for Rsubread. I will make it possible in development version soon. Keep you posted.

Jianhong.

ADD REPLY • link 3.8 years ago Ou, Jianhong ★ 1.3k

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Hi Jianhong,

Thank you for your reply! It's great! I will look forward to the update.

Best regards,

Alexandr

ADD REPLY • link 3.8 years ago alexandr.gopanenko ▴ 50

score 1 · Answer 1 · 2021-03-05

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Ou, Jianhong ★ 1.3k

@ou-jianhong-4539

Last seen 6 days ago

United States

Hi Alexandr,

In current release version, please try to use following parameters for library type: strandSpecific (0 (unstranded), 1 (stranded) and 2 (reversely stranded)) and for SE or PE: isPairedEnd (FALSE by default), countReadPairs (TRUE by default). For more information, please refer ?Rsubread::featureCounts

ADD COMMENT • link 3.8 years ago Ou, Jianhong ★ 1.3k

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Hi Jianhong,

Thank you very much for your response! I will try it soon!

Best regards,

Alexandr

ADD REPLY • link 3.8 years ago alexandr.gopanenko ▴ 50