Heat Map From Gff3

Question

[Florianino]

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!

[Neilfws]

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?

[Nibua]

Good question. Or your heatmap is just made to reflect the presence or not of an exon / intron / tRNA / ... ?

Answer 1

[Scott Cain]

I don't know if I would call it "easy" necessarily, depending on what your needs are, but there is a software project that is part of GMOD called GBrowse_karyotype:

http://gmod.org/wiki/GBrowse_karyotype

That works with the old release of GBrowse (version 1.70 or less). Installing it would be a lot of work to create just one or two pictures, but if it is for a larger project (particularly one that could make use of GBrowse as well), then this would be a reasonable thing to try.

Answer 2

[Nibua]

You may have a look to GenoViz viewer. It takes in account a huge variety of format and can plot heatmaps along chromosomes. If you want to plot quantitative data it's very easy to transform you GFF files into profiles.