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igvteam / hic-straw

Command line and web utilities for reading .hic contact matrix files
MIT License
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caught error while accessing GEO linked hic file #6

Closed lidaof closed 5 years ago

lidaof commented 5 years ago

Hi Jim,

Nice to see juicebox.js can access GEO hic files through web. I also tried this link with latest hic-straw (0.9.3), i got following error:

image

same links works at juicebox.js site. Did I miss any step? Thank you.

jrobinso commented 5 years ago

Sorry about that, I'll check it out.

On Thu, May 9, 2019 at 11:39 AM Daofeng Li notifications@github.com wrote:

Hi Jim,

Nice to see juicebox.js can access GEO hic files through web. I also tried this link https://ftp.ncbi.nlm.nih.gov/geo/samples/GSM2583nnn/GSM2583729/suppl/GSM2583729_H3K27ac_HiChIP_2.hic with latest hic-straw (0.9.3), i got following error:

[image: image] https://user-images.githubusercontent.com/102806/57478153-dc993b00-725f-11e9-8b0d-a250de7dac6a.png

same links works at juicebox.js site. Did I miss any step? Thank you.

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jrobinso commented 5 years ago

I can't reproduce this error, could you give me more details on how to reproduce it?

jrobinso commented 5 years ago

How were you using hic-straw (from node, script import, or es6 module)? I found a problem with the es6 module, its fixed in v0.9.4.

lidaof commented 5 years ago

Sorry Jim @jrobinso probably old code cached..i restarted node and see a new error: image

code is example code: image

Am I using the chr: All wrong way? Thank you :)

jrobinso commented 5 years ago

I'll look into it, "All" is not a real chromosome, as you know, and there is no data for the parameters you have entered, but it should give you a more reasonable error message than the one you see. Thanks for the test case, in the future could you insert code int a ``` block rather than a screenshot?

lidaof commented 5 years ago

i see @jrobinso sure, will do. Thanks for looking into this.

jrobinso commented 5 years ago

I'm going to add a special method to access "all-all". But could you tell me what you are going to do with the "all" data?

The real chromosomes should all work.

lidaof commented 5 years ago

Hi Jim @jrobinso , I don't really have such a use case yet. maybe when viewing genome wide interactions (like chr1->chr22)?

jrobinso commented 5 years ago

I'll add a method and special instructions for all-all, but I can't think of a use case for your browser. For interactions you probably will use bedPE files, you won't be able to see anything in the rotated hic maps at whole genome view.

lidaof commented 5 years ago

Thank you Jim @jrobinso