Plot SNPs on transcripts

Question

[g.papprank]

I have a bed file with transcript_chr/transcript_start/transcript_end/....../snp_pos/snp_type fields. Multiple SNPs may belong to the same transcript (so multiple rows may have the same trarnscript_start/transcript_end). I would like to use python or R to plot the transcripts maybe as rectangles and SNPs as points over the rectangles to see the distribution. Is there a specific tool (package) i could use for that (R or python)?

Thank You!

Answer 1

[colindaven]

GenomeGraphs might be helpful in R, check Fig 2 here

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-2