Annotate Genomic coordinates/ regions

Hi, I have recently finished small RNAseq analysis for my Arabidopsis mutants. The final output list has chromosome regions only (no Gene identifiers, Gene Symbols etc.). I want to annotate these regions to the corresponding genes, intergenic regions etc. Are there any programs in galaxy, R, or otherwise that allow me to do this. Any help is greatly appreciated.

Hi @Ubaid_Midhat,
what is the format of the dataset which contains the regions? Following this thread in GHelp, I suggest you use the Chipseeker tool. However, it requires a bedgraph file as input


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Hi @gallardoalba
I have a gff3 file with sRNA annotations (Chr#, Start and End positions, etc.) I looked into chipseeker tool and it seems like this might just do the trick but I am having trouble with my input file. Is there a way to convert gff3 file to bedgraph?
Thank you so much for your help.

Hi @Ubaid_Midhat,
you can do it in Galaxy in two steps: