Arabidopsis 1001G data in MatrixTubemap

[josiahseaman]

• [x] Identify data source: six_ref.GFA
• [x] Install / Compile ODGI
• [x] Process through ODGI
• [x] Process through Tubeify
• [x] Import into tubemap.js
• [x] Rendered and browsing (performant)
• [ ] Links verified correct
• [x] reasonable size 5 MB (larger binning for whole?)
• [x] Sebastian's data converted
• [ ] Sebastian's data visualized

[ekg]

Here's how to take a GFA file and make the tubmap bin input:

odgi build -g x.gfa -o - | odgi sort -i - -o x.og
odgi bin -i x.og -w $bin_width -j | gzip >x.og.$bin_width.json.gz

[josiahseaman]

Actual commands used:

cmake -H. -Bbuild && cmake --build build -- -j 3

./odgi build -g sixref_Chr4.gfa -o - | ./odgi sort -i - -o sixref_Chr4.og
bin_width=100000
./odgi bin -i sixref_Chr4.og -w $bin_width -j > sixref_Chr4.og.$bin_width.json.gz
bin_width=10000
./odgi bin -i sixref_Chr4.og -w $bin_width -j  >sixref_Chr4.og.$bin_width.json
bin_width=1000
./odgi bin -i sixref_Chr4.og -w $bin_width -j > sixref_Chr4.og.$bin_width.json
bin_width=100
./odgi bin -i sixref_Chr4.og -w $bin_width -j > sixref_Chr4.og.$bin_width.json

node.exe cli.js -j data\sixref_Chr4.og.10000.json --bin_length=10000 --tiles=1 --tile_json=data\sixref_Chr4.og.10000.tile.json
node.exe cli.js -j data\sixref_Chr4.og.1000.json --bin_length=1000 --tiles=1 --tile_json=data\sixref_Chr4.og.1000.tile.json
node.exe cli.js -j data\sixref_Chr4.og.100.json --bin_length=100 --tiles=1 --tile_json=data\sixref_Chr4.og.100.tile.json

[josiahseaman]

Real Arabidopsis data is working! I will definitely need #14 for this data, because it's very detailed and doesn't all fit into view easily.

Bin size = 100. translate(0,0) scale(0.0038, 2)

This is the entire Chr4 bins at bin size 1k. transform="translate(0,0) scale(0.038,1.9)"

Bin size 10k.

Interestingly, file size between the formats doesn't scale linearly. This tells me that at small bin sizes, (100.json) there are long runs of contiguous ids covered.

[josiahseaman]

Currently waiting on Sebastian for more data.