Dump/strawC for .hic files

[Vanessa Roy]

Dear All,

I have a few questions regarding the extraction of contact maps from .hic files.

I can't seem to be able to use juicer tools (dump command) or strawC on datasets uploaded on your website DNA zoo. I tried to get contact maps using the link to the dataset with dump / strawC, however, it doesn't seem to work. 

On the other hand, I have no problem using dump / strawC with the urls on the other website:

https://www.aidenlab.org/data.html

I can't seem to figure out why this is not working with files on the DNA zoo website. Is it possible to use the dump command / strawC with the files on the DNA zoo website? If so, could you point me in the right direction as to how I could extract contact maps from the DNA zoo website using the link to the .hic file?

Many thanks already in advance for your help!

Best regards

Vanessa Roy

[Neva Durand]

Hello Vanessa,

Have you tried downloading the file of interest and then running?

We are looking into your problem of accessing via URL.

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Assistant Professor |  Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org

[Olga Dudchenko]

Hello Vanessa,

Please specify what is the problem that you are experiencing. The files are hosted on dropbox, wasabi and s3. The links on the website are the dropbox links. Are you using the Dropbox url? What is the command that you are trying to run?

Olga

On Monday, January 25, 2021 at 8:50:59 AM UTC-6, Neva Durand wrote:

Hello Vanessa,

Have you tried downloading the file of interest and then running?

We are looking into your problem of accessing via URL.

On Mon, Jan 25, 2021 at 4:04 AM Vanessa Roy <vanes...@mail.tau.ac.il> wrote:

Dear All,

I have a few questions regarding the extraction of contact maps from .hic files.

I can't seem to be able to use juicer tools (dump command) or strawC on datasets uploaded on your website DNA zoo. I tried to get contact maps using the link to the dataset with dump / strawC, however, it doesn't seem to work. 

On the other hand, I have no problem using dump / strawC with the urls on the other website:

https://www.aidenlab.org/data.html

I can't seem to figure out why this is not working with files on the DNA zoo website. Is it possible to use the dump command / strawC with the files on the DNA zoo website? If so, could you point me in the right direction as to how I could extract contact maps from the DNA zoo website using the link to the .hic file?

Many thanks already in advance for your help!

Best regards

Vanessa Roy

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[Vanessa Roy]

The dump commands I tried to run (neither worked for me): 

java -jar juicer_tools.jar dump oe KR https://www.dropbox.com/sh/7z5qpl64oi2in6p/AAA8A3KDTppRcpGth3ytHC5Ea/AaegL5.0.hic?dl=0 1 1 BP 1000000 ./Aedes_1.txt

java -jar juicer_tools.jar dump oe KR https://www.dropbox.com/sh/7z5qpl64oi2in6p/AAA8A3KDTppRcpGth3ytHC5Ea/AaegL5.0.hic 1 1 BP 1000000 ./Aedes_1.txt

I also tried downloading the .hic file first and then replacing in the above code the url with the filename, but I got an error (NullPointerException).

with strawC, I tried the following:

result = strawC.strawC('KR', 'https://www.dropbox.com/sh/7z5qpl64oi2in6p/AAA8A3KDTppRcpGth3ytHC5Ea/AaegL5.0.hic?dl=0', '1', '1', 'BP', 1000000)  

result = strawC.strawC('KR', 'https://www.dropbox.com/sh/7z5qpl64oi2in6p/AAA8A3KDTppRcpGth3ytHC5Ea/AaegL5.0.hic', '1', '1', 'BP', 1000000)

But always got the error message:

Hi-C magic string is missing, does not appear to be a hic file

1 not found in the file.

However, for instance the following works fine for me:

java -jar juicer_tools.jar dump oe KR  https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_30.hic 1 1 BP 1000000 ./test.txt

result = strawC.strawC('KR', 'https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined_30.hic', '1', '1', 'BP', 1000000)

I am not sure what I am doing wrong or why it is not working.

Thanks for your help.

Best,

Vanessa

[Olga Dudchenko]

There is no chromosome one in this genome assembly. Please make sure you pass the correct chromosome names.

Best,

Olga

[wei...@gmail.com]

When working with juicer_tools.jar or straw the links to the hic file must provide the direct binary stream to the content. The Dropbox link ( https://www.dropbox.com/sh/7z5qpl64oi2in6p/AAA8A3KDTppRcpGth3ytHC5Ea/AaegL5.0.hic?dl=0 ) will provide an html web page with a link to download the file. This html file is not understood by juser_tools or straw. The trick with Dropbox links to get directly the content of the file and not an html, is to replace the "?dl=0" to "?dl=1" in the URL. Like this  https://www.dropbox.com/sh/7z5qpl64oi2in6p/AAA8A3KDTppRcpGth3ytHC5Ea/AaegL5.0.hic?dl=1

Best,

David

[Olga Dudchenko]

Hey David,

The hosting is not a primary problem in this thread.

Vanessa, when you are passing '1 1' to the files, straw is looking for chromosome 1. There is no such chromosome in this file. The first chromosome name is, e.g. NC_035107.1.

Olga

[Vanessa Roy]

Hi Olga, Hi David,

Many thanks for your help, both inputs were helpful. It is now working after I corrected the chromosome name and the link. 

Best,

Vanessa