chr_chr map ERROR

[awezmm]

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]

Make sure the chromosome name matches exactly.

On Fri, Apr 10, 2020 at 4:46 AM awezmm ***@***.***> 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/ — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#48>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAK2EW4VIZGAZCD3DF6K633RL3MHDANCNFSM4MFKB3ZA> .

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

[awezmm]

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]

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 ***@***.***> 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 <#48 (comment)>, 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