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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Does the "--nohp" option return siRNAs only? #101

Closed uceleste closed 3 years ago

uceleste commented 3 years ago

Dear developers,

I have installed and tested ShortStack using your test data. Everything worked perfectly. I just need a little confirmation. For my analysis I will only need siRNAs. For this reason I have not installed RNAfold and I have run the program with the "--nohp" option. So, can you confirm me that all the sequences reported in the gffs refer exclusively to siRNAs?

Thanks

MikeAxtell commented 3 years ago

Glad to hear it is working for you. If you run with --nohp the script will not be able to analyze whether or not any of the discovered clusters are MIRNAs or not. However you cannot thus conclude everything is siRNA. ShortStack only finds clusters of aligned sRNA reads. These could be microRNAs, siRNAs, degraded bits of longer RNAs, or any combination thereof. Caveat emptor.

-- Michael J. Axtell, Ph.D. Professor of Biology Pennsylvania State University https://sites.psu.edu/axtell https://plantsmallrnagenes.science.psu.edu

From: uceleste notifications@github.com Date: Wednesday, October 21, 2020 at 11:01 AM To: MikeAxtell/ShortStack ShortStack@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [MikeAxtell/ShortStack] Does the "--nohp" option return siRNAs only? (#101)

Dear developers,

I have installed and tested ShortStack using your test data. Everything worked perfectly. I just need a little confirmation. For my analysis I will only need siRNAs. For this reason I have not installed RNAfold and I have run the program with the "--nohp" option. So, can you confirm me that all the sequences reported in the gffs refer exclusively to siRNAs?

Thanks

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