Text Tracks

Tracks are usually prepared in binary format for efficient region access, like bigWig, bigBed, HiC and etc. Text file format is very flexible, thus caused some trouble for us to standardize the data input. While there are some circumstances that text track files could also be useful, it can be very convenient to just upload a text file and visualize the data on the browser without formatting the data to a binary format. Once added, text tracks can be very fast since there is no more network requests or transfers, also we have received requests that adding text files as tracks from our users.

bed

The most common text file would in bed format, like this one below:

chr1        13041   13106   reg1    1       +
chr1        753329  753698  reg2    2       +
chr1        753809  753866  reg3    3       +
chr1        754018  754252  reg4    4       +
chr1        754361  754414  reg5    5       +
chr1        754431  754492  reg6    6       +
chr1        755462  755550  reg7    7       +
chr1        761040  761094  reg8    8       +
chr1        787470  787560  reg9    9       +
chr1        791123  791197  reg10   10      +

Say if we have a text file named bed-text.txt with the content above. Open the Text Tracks menu:

_images/text_menu.png

This will bring the text track UI:

_images/bedtext_1.png

Choose bed as the text file type, the choose our text file:

_images/bedtext_2.png

After we submit this file, the track is added with the content of our text file:

_images/bedtext_3.png

bedGraph

bedGraph is also very common, it’s typically 4 columns bed file like below:

chr6        52155366        52155379        14
chr6        52155379        52155408        13
chr6        52155408        52155426        12
chr6        52155426        52155433        11
chr6        52155433        52155442        10
chr6        52155442        52155446        9
chr6        52155446        52155472        8
chr6        52155472        52155475        9
chr6        52155475        52155499        8
chr6        52155499        52155501        7

Choose bedGraph from the track track UI:

_images/bedgraph_text_1.png

The choose the bedGraph text file:

_images/bedgraph_text_2.png

The text track file is added:

_images/bedgraph_text_3.png

longrange

The longrange format can also be uploaded directly as text file, choose longrange in the text type dropdown menu:

_images/long_text_1.png

Choose the text file in longrange format:

_images/long_text_2.png

The track will be added as below (adjust region and display style as arc):

_images/long_text_3.png

customized long-range format

One of our user proposed a long-range format as below:

_images/long_text_4.png

We also added the support and file in this format can be loaded as track:

_images/long_text_5.png

Feel free to contact us if you need more formats supported.

What if the text file is huge?

If your text track is huge in size, convert to binary format is recommended. However, you can still use the text file if you want. Make sure you check the Use a Worker thread checkbox, the browser will use a background thread for text file loading.

_images/worker_check.png