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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Software to draw the dot-bracket RNA secondary structure #71

Closed sebel76 closed 6 years ago

sebel76 commented 6 years ago

Dear Micheal,

I run the ShortStack program to mapping sRNA reads on genome and predict novel miRNA candidates. I want to represent the dot-bracket predicted hairpin structure.

Do you have any recommendation of nice and easy to use software that can draw the hairpin structure using the ShortStack output?

Thanks and best regards, Sébastien

MikeAxtell commented 6 years ago

You could try strucVis -- https://github.com/MikeAxtell/strucVis. It takes coordinates, a genome file, a bam file of small RNA alignments, and produces a postscript file of the predicted RNA secondary structure where each nt is color-coded by depth of sRNA-seq coverage.

On Fri, Feb 16, 2018 at 11:27 AM, sebel76 notifications@github.com wrote:

Dear Micheal,

I run the ShortStack program to mapping sRNA reads on genome and predict novel miRNA candidates. I want to represent the dot-bracket predicted hairpin structure.

Do you have any recommendation of nice and easy to use software that can draw the hairpin structure using the ShortStack output?

Thanks and best regards, Sébastien

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