Hello,

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!

Thanks a lot!