Custom Hi-C data

[will-NYGC]

I have some hi-C data that i formatted into this format shown on the wiki: chr1,713605,715737 chr1,720589,722848 2

but it crashes everytime I try to upload. I don' t think they're too big, ~15Mb, as it's only a low depth test run. Any suggestions how to see my data on your browser? thanks.

[lidaof]

Hi @will-NYGC , do you mind put few lines of your data here for us to debug? Thanks.

[will-NYGC]

I’ve tried both formats ftp://ftp.nygenome.org/data2/Sample_Astro_2607_1000000_iced.bed and ftp://ftp.nygenome.org/data2/Sample_Astro_2607_1000000_iced.bg

do i need integer only scores?

On Feb 22, 2016, at 3:57 PM, Daofeng Li notifications@github.com<mailto:notifications@github.com> wrote:

Hi @will-NYGChttps://github.com/will-NYGC , do you mind put few lines of your data here for us to debug? Thanks.

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[lidaof]

Hi @will-NYGC, for the first example of your file, do you use bgzip to compress and tabix to index (see http://wiki.wubrowse.org/Long-range)? We are testing your 2nd example and will let you know.

[will-NYGC]

Yea I tried with index. It loads but I don’t see any data. I thought maybe it was my data but I couldn’t tell b/c the other file won’t load at all. any help would be appreciated.

will

On Feb 23, 2016, at 1:04 PM, Daofeng Li notifications@github.com<mailto:notifications@github.com> wrote:

Hi @will-NYGChttps://github.com/will-NYGC, for the first example of your file, do you use bgzip to compress and tabix to index (see http://wiki.wubrowse.org/Long-range)? We are testing your 2nd example and will let you know.

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[lidaof]

If you submit URL has this tabix'ed track file, it should be loaded. do you try refresh cache on this track if you didn't see any data displayed? Or use a different file name? can you send me the URL as well?

The 2nd option using file upload is not recommended since it's support limited file size, while seems we have some issues for this function now and I am finding out why. Thank you Will.

[will-NYGC]

ok… i’ll stick with URL option.

ftp://ftp.nygenome.org/data2/Sample_Astro_2607_1000000_iced.bed.gz

I’m not sure why I load it in (with new name) and nothing shows up even if I navigate to specific locations copied from file that definitely have data: chr1 2000000 3000000 chr1:3000000-4000000,235.962856 207 +

thank you, Daofeng, for your help.

On Feb 23, 2016, at 2:12 PM, Daofeng Li notifications@github.com<mailto:notifications@github.com> wrote:

If you submit URL has this tabix'ed track file, it should be loaded. do you try refresh cache on this track if you didn't see any data displayed? Or use a different file name? can you send me the URL as well?

The 2nd option using file upload is not recommended since it's support limited file size, while seems we have some issues for this function now and I am finding out why. Thank you Will.

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[lidaof]

Hi Will,

sorry for late response, was just back from a meeting. I tried your URL and it works pretty well though, do you tried zoom out a little bit for the data to be displayed?

[will-NYGC]

oh wow. ok great. i must be doing something wrong but glad to see file is fine. i’ll keep trying. thanks so much for your help.

will

On Feb 23, 2016, at 3:26 PM, Daofeng Li notifications@github.com<mailto:notifications@github.com> wrote:

Hi Will,

sorry for late response, was just back from a meeting. I tried your URL and it works pretty well though, do you tried zoom out a little bit for the data to be displayed?

[image]https://cloud.githubusercontent.com/assets/102806/13265569/400b4d6c-da39-11e5-8630-af927e7b6f72.png

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