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MikeAxtell / ShortStack

ShortStack: Comprehensive annotation and quantification of small RNA genes
MIT License
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Annotation of sRNA loci #104

Closed midhatubaid closed 1 year ago

midhatubaid commented 3 years ago

Dear Dr. Axtell, I have just finished sRNA analysis for Arabidopsis using ShortStack 3.3 (on cyverse.org). In order to identify different sRNA subclasses, I used the Arabidopsis sRNA loci file (https://plantsmallrnagenes.science.psu.edu/genomes.php?id=50). Since this reference loci file has genomic coordinates but does not have the corresponding genomic features (e.g. gene, promoter, UTR, intergenic region, etc.), I want to annotate the resulting count files also with genomic features corresponding to genomic coordinates from the ath-b10 genome build. Could you please let me know what program you use to annotate these genomic intervals?

MikeAxtell commented 1 year ago

This is not a ShortStack question. NCBI datasets, phytozome, and Arabidopsis.org are 3 examples of locations where genomic datasets can be acquired for Arabidopsis thaliana.