.hic file resolution

[tguuu...@gmail.com]

Dear Neva,

I am interested in "juicer tools". I am curious about the .hic file resolution. If I have a hic file produced by juicer tool "pre" command without defined the resolution parameters, could I transform this .hic file to other resolution .hic file, such as 20kb, 10kb or 40kb?

Thank you!

Best,

Garen

[Neva Durand]

Hello Garen,

It's not currently possible to do this with the Pre command.  We are looking into modifications to the file format that would make this easier.

Note that from the contact list, you can use Pre to make a hic file at arbitrary resolutions using the "-r" flag.

Best

Neva

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Neva Cherniavsky Durand, Ph.D.

Staff Scientist, Aiden Lab

www.aidenlab.org

[Steve Gisselbrecht]

Hi, Neva.

I attempted to modify the juicer.sh script so that, when it calls Pre, it would add higher resolutions to the .hic file, and I got the following error message:

Exception in thread "main" jargs.gnu.CmdLineParser$UnknownOptionException: Unknown option '-r'

I had added (to the pre commands in the script) the following flag, trying both with and without the quotes:

-r "100000,50000,25000,10000,5000,2500,1000"

Any ideas why this did not work?

Thank you!

On Tuesday, November 14, 2017 at 8:43:36 AM UTC-5, Neva Durand wrote:

Hello Garen,

It's not currently possible to do this with the Pre command.  We are looking into modifications to the file format that would make this easier.

Note that from the contact list, you can use Pre to make a hic file at arbitrary resolutions using the "-r" flag.

Best

Neva

On Mon, Nov 13, 2017 at 9:28 PM, <tguuu...@gmail.com> wrote:

Dear Neva,

I am interested in "juicer tools". I am curious about the .hic file resolution. If I have a hic file produced by juicer tool "pre" command without defined the resolution parameters, could I transform this .hic file to other resolution .hic file, such as 20kb, 10kb or 40kb?

Thank you!

Best,

Garen

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[Neva Durand]

Hello,

Be sure you are using the latest jar, found here:  https://github.com/theaidenlab/juicer/wiki/Download

Best

Neva

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