1D annotation with specified color and score

[Hurley Li]

Dear Juicebox team,

I would like to create a 1D annotation bed file, with customized color and score (height of the bar, like those represent eigenvectors). I can't figure out what columns should I put these information in the bed file. Could you please advise?

Thanks!

Hurley

 

[Neva Durand]

Hello,

We use the .wig file format for eigenvectors, but you can use BED with score as well.

You can read more about different formats here:

https://genome.ucsc.edu/FAQ/FAQformat

We support all the formats that IGV supports:

http://software.broadinstitute.org/software/igv/

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Hurley Li]

Dear Neva, 

I still have trouble loading a bedgraph file into juicebox. 

Here's what I have in my file

track type=bedGraph

chr1 0 1000000 -0.0227036194528986

chr1 1000000 2000000 -0.0880239726030334

chr1 2000000 3000000 -0.0454658244602945

chr1 3000000 4000000 -0.0417887907953985

chr1 4000000 5000000 0.00467185019760866

chr1 5000000 6000000 0.000682791239575303

chr1 6000000 7000000 -0.0812863427397008

chr1 7000000 8000000 -0.0866944781181945

chr1 8000000 9000000 -0.0876335418148131

chr1 9000000 10000000 -0.0952796488636748

I tried with or without header, I also tried give different extensions for the file name, .bedgraph, .bdg, .bedGraph .... but got no luck

The error message I got is "Could not load resource null"

Do you have any idea what might cause this problem?

Thanks!

Hurley

On Friday, March 3, 2017 at 4:43:01 AM UTC-8, Neva Durand wrote:

Hello,

We use the .wig file format for eigenvectors, but you can use BED with score as well.

You can read more about different formats here:

https://genome.ucsc.edu/FAQ/FAQformat

We support all the formats that IGV supports:

http://software.broadinstitute.org/software/igv/

Best

Neva

On Thu, Mar 2, 2017 at 11:06 PM, Hurley Li <lihe....@gmail.com> wrote:

Dear Juicebox team,

I would like to create a 1D annotation bed file, with customized color and score (height of the bar, like those represent eigenvectors). I can't figure out what columns should I put these information in the bed file. Could you please advise?

Thanks!

Hurley

 

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[Hurley Li]

Weird thing is I can load this bedgraph file with the Rao & Huntley GM12878 .hic map, but not with my own .hic map. I noticed a difference in my .hic map is I used assembly name chr1, chr2 .... instead of just 1,2 ... Do you think that might be the reason causing this problem? 

Thanks!

Hurley

[Neva Durand]

Hello Hurley,

Yes, this is possibly the problem; what did you name your chrom.sizes file?  Could you send it?

Thanks,

Neva

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[yonghao sun]

Hi, I also got the same problem when I loaded the wig or bed file in juicebox. The output was "Could not load resource null" or I can load in but the 1D track show like below: just a band ,no score show.

Do you solve this problem?Thank you!
在 2017年3月11日星期六 UTC+8上午2:02:49，Hurley Li写道：

[yonghao sun]

I have solve it , Use wig file which in fixedStep header.

在 2019年7月29日星期一 UTC+8上午10:08:22，yonghao sun写道：