Datasources

Public datasources

TADues provide public datasources that can be used to create a track of plots. This includes all Hi-C datasources. Since Hi-C datasources are large they can be uploaded only upon request. List of public datasets are available on https://tadeus2.mimuw.edu.pl/datasources/).

If you have wish to upload any dataset new Hi-C data please contact Admin (b.poszewiecka@mimuw.edu.pl) to set the transfer of your files.

Private datasources

Users can upload their own datasource in BED3, BED6, BED9, BED12 or BEDGraph format.

Short film showing how to upload data to TADeus2:

Subsequent fileds of BED file are:

  1. Chromosome
  2. Chromosome start coordinate
  3. Chromosome end coordinate
  4. Name of record
  5. Score of record
  6. Strand ('+' or '-' or'.')
  7. The starting position of the record
  8. The ending position of the record
  9. Color in RGB
  10. Number of blocks
  11. Comma-separated list of block sizes
  12. Comma-separated list of block starts

Examples of records in BED and BEDGRAPH formats that can be uploaded to TADeus2:

Bed3 format example:
chr1	100	200
chr2	300	500
Bed6 format example:
chr1	100	200	name1	10	+
chr2	300	500	name2	12	-
Bed9 format example:
chr1	100	200	name1	10	+	100	200	255,0,0
chr2	300	500	name2	12	-	300	500	0,255,0
Bed12 format example:
chr1	100	200	name1	10	+	100	200	255,0,0 2	20,50	100,150
chr2	300	500	name2	12	-	300	500	0,255,0	2	10,20	300,480
Bedgraph format example:
chr1	100	200	1.2
chr2	300	500	2.5

To create a private datasource select the "Datasource" menu option. Then click on the "Create from text input" or "Create from file" button and complete the form specifying the name of the datasource and the assembly. Remember that the chosen assembly must match the plot assembly. Depending on the input method, provide a file with datasource or paste in the data.

Figure 1. "Datasource" form