Question: Genomic feature graph
0
gravatar for jb.sequence
2.0 years ago by
jb.sequence0 wrote:

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.

ADD COMMENTlink written 2.0 years ago by jb.sequence0
1

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.

ADD REPLYlink written 2.0 years ago by Devon Ryan90k
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