Unknown chromosome error with eigenvector

[maryawood]

Hello, I'm trying to use eigenvector to predict A/B compartments and I'm getting an "Unknown chromosome" error. I've prepared my references files following the instructions here, and the chromosome I'm specifying is definitely in my reference. Any idea what might be causing this? Thanks!

[maryawood]

Hi, I just wanted to follow up on this. For reference, the here is the command I'm using and the error I am getting:

$ java -jar ~/PGTools/juicer/scripts/common/juicer_tools.jar eigenvector NONE sample.hic "NC_000067.6" BP 100000 test_eigen.txt Unknown chromosome: NC_000067.6

This is using a .hic file based on alignment to this assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26/

[nchernia]

Have you looked at the hic file in Juicebox? You will see the chromosomes it thinks are in the file. You can also use read_hic_header.py in the misc folder of Juicer.

On Tue, Apr 6, 2021 at 5:12 PM Mary Wood @.***> wrote:

Hi, I just wanted to follow up on this. For reference, the here is the command I'm using and the error I am getting:

$ java -jar ~/PGTools/juicer/scripts/common/juicer_tools.jar eigenvector NONE sample.hic "NC_000067.6" BP 100000 test_eigen.txt Unknown chromosome: NC_000067.6

This is using a .hic file based on alignment to this assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001635.26/

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/220#issuecomment-814443448, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EW6B7DTFBEAEAZSCJD3THN2NTANCNFSM42DH3ARQ .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[maryawood]

Hmm, it doesn't look like that script exists in the misc folder. I did just confirm that the chromosome is present when I view the Hi-C file in Juicebox (unless there is a different place I should be looking besides the scaffold names). Is there anything else I can try?

[nchernia]

Sorry it’s in the straw repository https://github.com/aidenlab/straw/tree/master/python

You could also try straw or juicer tools dump to see if those tools know about the scaffold.

On Tue, Apr 6, 2021 at 6:32 PM Mary Wood @.***> wrote:

Hmm, it doesn't look like that script exists in the misc folder. I did just confirm that the chromosome is present when I view the Hi-C file in Juicebox (unless there is a different place I should be looking besides the scaffold names). Is there anything else I can try?

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/aidenlab/juicer/issues/220#issuecomment-814477836, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAK2EW2DRRAZOGD5UNUDPB3THODXTANCNFSM42DH3ARQ .

-- Neva Cherniavsky Durand, Ph.D. | she, her, hers Assistant Professor | Molecular and Human Genetics Aiden Lab | Baylor College of Medicine www.aidenlab.org

[maryawood]

Thanks! With straw I was able to figure out that chromosomes weren't being detected in that version of the .hic file, which was unpartitioned. In the partitioned version of my .hic file, the chromosomes are detectable, and I am able to run eigenvector without issues. I really appreciate your help!

[laramiemckenna]

Hi @maryawood and @nchernia -- I am encountering the same issue! How do you recommend partitioning the .hic file?