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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Target prediction with siRNA clusters #79

Closed jana33 closed 3 years ago

jana33 commented 6 years ago

Hi Mike,

firstly thanks for writing such useful software, it is doing a great job on my small RNA data sets.

I have a question regarding the target prediction of siRNA clusters with valid dicer calls that do not follow miRNA rules. I am working with a fungus where there are very few predicted miRNAs, but a heap of highly expressed siRNA clusters and the most abundant read is predominantly 22 nts. For miRNA clusters, one would pick the most abundant read and proceed to target prediction. What would you recommend for siRNA clusters? Is it still valid to proceed with only the most abundant read returned by ShortStack for the cluster? Or would you use samtools to get all the reads from the cluster and use them all for target prediction?

Thanks!

MikeAxtell commented 6 years ago

Thank you for your question. I'm not familiar enough with siRNA functions in fungi to give an answer, I'm afraid. My hunch is that any method you use to find potential targets would ultimately need to be supported by experimental data showing that the predicted target really was targeted in vivo, something that is far beyond what ShortStack can do.

All the best, Mike Axtell

On Wed, Aug 8, 2018 at 12:39 AM jana33 notifications@github.com wrote:

Hi Mike,

firstly thanks for writing such useful software, it is doing a great job on my small RNA data sets.

I have a question regarding the target prediction of siRNA clusters with valid dicer calls that do not follow miRNA rules. I am working with a fungus where there are very few predicted miRNAs, but a heap of highly expressed siRNA clusters. For miRNA clusters, one would pick the most abundant read and proceed to target prediction. What would you recommend for siRNA clusters? Is it still valid to proceed with only the most abundant read returned by ShortStack for the cluster? Or would you use samtools to get all the reads from the cluster and use them all for target prediction?

Thanks!

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