Supported Format Conversion

Determine the file format

User Supplied

The user may choose which type each of the file is on the front end. This option has highest priority.

File Extension

The track type is first guessed from the file extension. Expected file extensions are: bed, bigbed, …

File Content

If the file extension does not indicate file type, the service can try its best to figure out the file format.

Conversion Process

BedGraph -> BigWig

By UCSC Kent Tool - BedGraphToBigWig

Wig -> BigWig

By UCSC Kent Tool - WigToBigWig

Bismark cov file -> Methylc Track

The cov file is converted to methylc (a bed-like) format by python script. For hg38, the service can tell which strand cytosine is on. For all other genome, the service assumes all cytosines are on positive strand.

Example cov lines are below:

chr1        10004   10004   0       0       2
chr1        10006   10006   66.6    20      10
chr1        10008   10008   100     1       0

Example methylc lines are below:

chr1        10004   10004   CG  0.00        +       2
chr1        10006   10006   CG  66.6        -       30
chr1        10008   10008   CG  100.        +       1

Bed like format

Sorted, and processed by tabix.

Processed files

They are uploaded, and served to browser directly. Example: bigwig, bigbed, hic