Able to plot only exons?

harbourlab / SparK

Publication quality NGS track plotting

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Able to plot only exons? #9

Closed katiearacena closed 3 years ago

katiearacena commented 3 years ago

Hello, thank you for the awesome plotting tool! I am wondering if it is possible to only plot RNAseq reads mapping to exons. Perhaps I can subset on this using the GTF file similar to plotting just one transcript?

harbourlab commented 3 years ago

Hi! I'm happy you find this useful :) You should be able to do this with bedtools intersect. Check it out here.. https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html#bed-output-bed-format-when-using-bam-input Only thing you need is a bed file that contains your exons, and you could intersect it with the RNAseq Bedgraph.

katiearacena commented 3 years ago

Success! Thank you very much for pointing me in the right direction!

harbourlab commented 3 years ago

Perfect! Glad it works out! Always looking forward to see more SparK plots! ;) Reach out any time!