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aidenlab / straw

Extract data quickly from Juicebox via straw
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chr_chr map ERROR #48

Open awezmm opened 4 years ago

awezmm commented 4 years ago

Hi, I am using straw with the following command: ./straw NONE myfile.hic Y:1:15902555 Y:1:15902555 BP 100000 > outfile I get following error: "File doesn't have the given chr_chr map."

However, I am able to clearly visualize the data on those same exact coordinates from that file on https://www.aidenlab.org/juicebox/

nchernia commented 4 years ago

Make sure the chromosome name matches exactly.

On Fri, Apr 10, 2020 at 4:46 AM awezmm notifications@github.com wrote:

Hi, I am using straw with the following command: ./straw NONE myfile.hic Y:1:15902555 Y:1:15902555 BP 100000 > outfile I get following error: "File doesn't have the given chr_chr map."

However, I am able to clearly visualize the data on those same exact coordinates from that file on https://www.aidenlab.org/juicebox/

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-- Neva Cherniavsky Durand, Ph.D. Pronouns: she, her, hers Assistant Professor, Aiden Lab www.aidenlab.org

awezmm commented 4 years ago

I compiled the hic file with pre from juicer tools. Wouldn't the chromosome name be 1-19, X, and Y? Furthermore when I do Y:1:15902555 Y:1:15902555 on the online juicebox visualizer I can see visualize the matrix with no errors. When I do the same coordinates with straw I get "File doesn't have the given chr_chr map." error.

Isn't the chromosome name in Y:1:15902555 Y:1:15902555 simply "Y"?

Furthermore, I thought an error in chromosome name gives the other error "One of the chromosomes wasn't found in the file. Check that the chromosome name matches the genome."

nchernia commented 4 years ago

It's possibly stored as "chrY chrY".

I don't see the other error in the C code - could you be sure to pull the latest? We've done some bug fixes over the past couple of months.

On Fri, Apr 10, 2020 at 10:26 PM awezmm notifications@github.com wrote:

I compiled the hic file with pre from juicer tools. Wouldn't the chromosome name be 1-19, X, and Y? Furthermore when I do Y:1:15902555 Y:1:15902555 on the online juicebox visualizer I can see visualize the matrix with no errors. When I do the same coordinates with straw I get "File doesn't have the given chr_chr map." error.

Isn't the chromosome name in Y:1:15902555 Y:1:15902555 simply "Y"?

Furthermore, I thought an error in chromosome name gives the other error "One of the chromosomes wasn't found in the file. Check that the chromosome name matches the genome."

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/aidenlab/straw/issues/48#issuecomment-612301389, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EWYBM4D2HBUA7BTOUU3RL7IOFANCNFSM4MFKB3ZA .

-- Neva Cherniavsky Durand, Ph.D. Pronouns: she, her, hers Assistant Professor, Aiden Lab www.aidenlab.org