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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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microRNA clusters #72

Closed BioFalcon closed 6 years ago

BioFalcon commented 6 years ago

Hi Michael, I have a question regarding microRNA clusters,

is the search of miRNAs dependant of pad size? so that if two pre-miRNAs that are close in the genome might end up being reported just as a cluster and not as pre-miRNAs.

Best ~FF

MikeAxtell commented 6 years ago

Hi Francisco,

Thanks for your message. Yes, unfortunately, if ShortStack gets too "greedy" and merges two closely spaced MIRNAs into one cluster, it definitely won't decide both of them are MIRNAs. Most of the time it probably won't even describe one of the two as MIRNAs. Yes, it's the pad size that determines this.

Cheers, Mike

On Mon, Mar 5, 2018 at 4:29 PM, Francisco Falcon notifications@github.com wrote:

Hi Michael, I have a question regarding microRNA clusters,

is the search of miRNAs dependant of pad size? so that if two pre-miRNAs that are close in the genome might end up being reported just as a cluster and not as pre-miRNAs.

Best ~FF

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BioFalcon commented 6 years ago

Thanks for your answer Mike, So a lower pad size would be recommended to find microRNAs?

Best, ~FF

MikeAxtell commented 6 years ago

Not necessarily. I tried hard to get the default setting optimized. That said, if you do find that obviously tandem miRNAs are not being found correctly, lowering pad would be a good thing to try. The trade off is that with lower values of pad you will begin to "over-split" other clusters.

On Thu, Mar 8, 2018 at 4:16 PM, Francisco Falcon notifications@github.com wrote:

Thanks for your answer Mike, So a lower pad size would be recommended to find microRNAs?

Best, ~FF

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-- Michael J. Axtell, Ph.D. Professor of Biology Penn State University http://sites.psu.edu/axtell