I'd like to draw heat maps for several chromosomes of one genome using GFF3 files. I have GFF3 for genes with multiple lines for each gene (introns, exons...) as well as GFF3 for other features with 1 line for each (e.g. tRNA). GFF2PS does not look obvious at all. Would anyone know an easy way to proceed? The heat map could use gray scale or ideally colors.
The GFF3 would be typically as follows
scaffold_10000 SSRs match 167 184 0.0 + . ID=ms1549910_scaffold_10000_C17;Target=C17+1+18 scaffold_10000 SSRs match_part 167 184 0.0 + . ID=mp1549910-1_scaffold_10000_C17;Parent=ms1549910_scaffold_10000_C17;Target=C17+1+18 scaffold_10000 SSRs match_part 167 184 0.0 + . ID=mp1549910-2_scaffold_10000_C17;Parent=ms1549910_scaffold_10000_C17;Target=C17+1+18 scaffold_10000 SSRs match 232 254 0.0 + . ID=ms1549911_scaffold_10000_GGCTTGAAGGGC2;Target=GGCTTGAAGGGC2+1+23 scaffold_10000 SSRs match 325 339 0.0 + . ID=ms1549912_scaffold_10000_CAG6;Target=CAG6+1+15 scaffold_10000 SSRs match 363 384 0.0 + . ID=ms1549913_scaffold_10000_CGC7;Target=CGC7+1+22 scaffold_10000 SSRs match_part 363 384 0.0 + . ID=mp1549913-1_scaffold_10000_CGC7;Parent=ms1549913_scaffold_10000_CGC7;Target=CGC7+1+22 scaffold_10000 SSRs match_part 365 384 0.0 + . ID=mp1549913-2_scaffold_10000_CGC7;Parent=ms1549913_scaffold_10000_CGC7;Target=CGC7+1+20 scaffold_10000 SSRs match 551 569 0.0 + . ID=ms1549914_scaffold_10000_CCAGCAGCA2;Target=CCAGCAGCA2+1+19 scaffold_10000 SSRs match 615 636 0.0 + . ID=ms1549915_scaffold_10000_CAG7;Target=CAG7+1+22 scaffold_10000 SSRs match_part 615 636 0.0 + . ID=mp1549915-1_scaffold_10000_CAG7;Parent=ms1549915_scaffold_10000_CAG7;Target=CAG7+1+22 scaffold_10000 SSRs match_part 627 636 0.0 + . ID=mp1549915-2_scaffold_10000_CAG7;Parent=ms1549915_scaffold_10000_CAG7;Target=CAG7+1+10
but using BED would be fine as well or any other format that can be obtained from GFF3
Thanks a lot!
Heat maps are for visualization of quantitative data. What quantitative data do you have in your GFF file? Can you provide some sample lines from the file?
Good question. Or your heatmap is just made to reflect the presence or not of an exon / intron / tRNA / ... ?