Able to plot only exons?
katiearacena opened this issue · 3 comments
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?
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.
Success! Thank you very much for pointing me in the right direction!
Perfect! Glad it works out! Always looking forward to see more SparK plots! ;) Reach out any time!