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.
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:
This will bring the text track UI:
Choose bed as the text file type, the choose our text file:
After we submit this file, the track is added with the content of our text file:
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:
The choose the bedGraph text file:
The text track file is added:
The longrange format can also be uploaded directly as text file, choose longrange in the text type dropdown menu:
Choose the text file in longrange format:
The track will be added as below (adjust region and display style as arc):
customized long-range format¶
One of our user proposed a long-range format as below:
We also added the support and file in this format can be loaded as track:
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.