Genomic feature graph
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4.0 years ago

Hello,

I am rather new to bioinformatics (PhD student) and am stuck on a particular part of the pipeline my advisor and I are setting up. I am essentially trying to put together a genomic feature graph that includes promoter, TSS, intron, exon, intergenic, 5'UTR, 3'UTR, and CDS. We want the final output to be a stacked bargraph with percentages. I was able to find a gtf annotations from gencode which has gene, exon, transcript, start_codon, stop_codon, 5'UTR, 3'UTR, and CDS. From the looks of it, it seems I have everything except promoter, intron, and intergenic and would eventually need to remove gene and transcript since they overlap several features. Also, do I also need to account for the overlap of CDS with exon in the gtf file. How would I go about this as far as scripting goes?

I would really like to use this with featureCounts as it is a rather straight forward program.

sequencing bisulfite sequencing featureCounts • 1.3k views
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I'd need to see an example to know exactly what you want, but you may find that plotEnrichment from deepTools does most of what you want.

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