Delta supports two ways to upload custom data. One is to upload pre-calculated loop,TAD and 3D physical model, the other is to upload the Contact matrix data.
1.Upload pre-calculated data
Upload any files in given format regarding the interaction loop, TAD and 3D model for visualization. The required formats are described below.
2.Upload Contact matrix
Delta tool applies TADtree, FastHiC to call interaction loop and TAD respectively. It constructs 3D model based on the uploaded contact matrix using BACH / HSA / MOGEN.
1)The supported Contact matrix file format
Example.
11 197 175 154 140 147
197 11 210 138 124 98
175 210 33 348 143 110
154 138 348 44 176 171
140 124 143 176 55 448
147 98 110 171 448 66
11 197 175 154 140 147
197 11 210 138 124 98
175 210 33 348 143 110
154 138 348 44 176 171
140 124 143 176 55 448
147 98 110 171 448 66
2)The supported interaction loop file format: GFF3.
Example.
11 hic arc 4600000 5050000 . . . ID=87;Name=87;Note=11:4600000-4650000|11:5000000-5050000
11 hic arc 4600000 5100000 . . . ID=88;Name=88;Note=11:4600000-4650000|11:5050000-5100000
11 hic arc 4600000 5150000 . . . ID=89;Name=89;Note=11:4600000-4650000|11:5100000-5150000
11 hic arc 4600000 5050000 . . . ID=87;Name=87;Note=11:4600000-4650000|11:5000000-5050000
11 hic arc 4600000 5100000 . . . ID=88;Name=88;Note=11:4600000-4650000|11:5050000-5100000
11 hic arc 4600000 5150000 . . . ID=89;Name=89;Note=11:4600000-4650000|11:5100000-5150000
3)The supported TAD file format: GFF3.
Example.
11 hic tad 4500000 4650000 . . . ID=1;Name=1
11 hic tad 5300000 5450000 . . . ID=2;Name=2
11 hic tad 5450000 5650000 . . . ID=3;Name=3
11 hic tad 6200000 6400000 . . . ID=4;Name=4
11 hic tad 4500000 4650000 . . . ID=1;Name=1
11 hic tad 5300000 5450000 . . . ID=2;Name=2
11 hic tad 5450000 5650000 . . . ID=3;Name=3
11 hic tad 6200000 6400000 . . . ID=4;Name=4
4)The supported 3D model file format: XYZ, JSON.
Example.
5
BACH OUTPUT
C 0.0000 0.0000 0.0000 11:4500000..4550000
C 0.1056 0.0000 0.0000 11:4550000..4600000
C 0.2047 0.0229 0.0000 11:4600000..4650000
C 0.2698 0.1251 0.0544 11:4650000..4700000
C 0.2780 0.1991 0.1230 11:4700000..4750000
Line 1 is the bead numbers.
Line 2 is a description information.
Line 3-7 are the positions of beads. Each bead starts with Carbon element, and follows the X,Y,Z position. The last field is the genome position of this bead.
5
BACH OUTPUT
C 0.0000 0.0000 0.0000 11:4500000..4550000
C 0.1056 0.0000 0.0000 11:4550000..4600000
C 0.2047 0.0229 0.0000 11:4600000..4650000
C 0.2698 0.1251 0.0544 11:4650000..4700000
C 0.2780 0.1991 0.1230 11:4700000..4750000
Line 1 is the bead numbers.
Line 2 is a description information.
Line 3-7 are the positions of beads. Each bead starts with Carbon element, and follows the X,Y,Z position. The last field is the genome position of this bead.