how can I road my files?

[TakatoG]

Hi,
I made a washU.txt file from CHiCAGO, so I loaded it in WashU browser.
However, it remained blank...

How can I my files to load??
I manipulated Tracks>Local text tracks.

Thank you.

[lidaof]

Hi @TakatoG wondering if your file contains 1, 2, 3 as chrom name, should be chr1, chr2 etc? if not, can you send me your file (or part of it)? thanks!

[TakatoG]

Hi!
Thank you for your replay. I'm a a beginner of bioimformatics..

I tested CHiCAGO's file as follows;
https://www.bioconductor.org/packages/release/bioc/vignettes/Chicago/inst/doc/Chicago.html

and I got .txt file.

(_washU_text.txt)

Can I load this?
Thank you.

[lidaof]

Hi @TakatoG ,

Sorry for late reply. Current this format is not supported directly, but can be added easily in next release.
if you can do scripting, you can convert your file to the follow below:

chr1    713605  715737  chr1:720589-722848,2
chr1    717172  720090  chr1:761197-762811,2
chr1    720589  722848  chr1:713605-715737,2
chr1    755977  758438  chr1:758539-760203,2

then you can load the reformatted text file through: Tracks-> Local text tracks-> choose long-range text

Hope this helps. I will add the direct support in next release (a week or two).

[TakatoG]

Thank you for reply.
Is it possible that convert the file?
Could you tell me how to convert the file?

Thank you.

[lidaof]

Hi @TakatoG ,

you can use this one line command to convert the format:

 sed 's/\t/,/2;s/,/\t/;s/,/\t/;s/,/:/;s/,/-/;' _washU_text.txt > long-range.txt

then you can upoad this file to the browser using the local text tracks, then navigating to some positions on chr20, below is your data displayed on the browser:

[TakatoG]

Hi,
Thank you very much for teaching me!
However do you know why this happen??

[lidaof]

this is called heatmap style, you can right click and switch to arc style

[TakatoG]

Hi.
Thank you for teaching me!
Really appreciate.