Question: Reference genome annotations in IGB
1
gravatar for James.Connolly
2.0 years ago by
James.Connolly10 wrote:

Hi there,

I have managed to generate ChIP-seq data using MACS in GALAXY and can view the resulting .wig and .bed files in IGB no problem. However, I am having trouble figuring out how to add annotations (say from a genbank file) to the reference genome so I can browse the binding sites. I have tried to create a custom reference synonym file using this protocol (https://wiki.transvar.org/display/igbman/View+a+bacterial+genome+in+IGB) but still cannot merge my ChIP-seq data with the resulting annotated reference.

I have also tried importing data that is useable with a built in genome in IGB and the same problem occurs.

Could anyone point me in the direction of how to add genbank annotations to a reference track?

Apologies for the basic question but I am new to both ChIP-seq and IGB and still getting to grips with things. Any help is appreciated.

Cheers

igb chip-seq • 714 views
ADD COMMENTlink modified 2.0 years ago by Mason Meyer110 • written 2.0 years ago by James.Connolly10
1
gravatar for Mason Meyer
2.0 years ago by
Mason Meyer110
United States
Mason Meyer110 wrote:

Hello,

My name is Mason Meyer, IGB Support Specialist. Thank you for taking the time to post your question on Biostars so that we can help resolve the issue you are experiencing. Other users have also experienced the issue you are currently facing, and our team is working to improve the user experience related to this. Sometimes what happens is that a user has data, such as your ChIp-seq data, that has been created using a different genome version than the reference genome that the user is trying to use in IGB. If you believe that this is not the case, then there may be something else going on and it may help if I can use your files for testing this issue. Do you think this is possible? If so, it may be best to contact us via the email address on our IGB Support Page. This way you could e-mail your files directly to us, if you are able to. I understand if you are not able to though, but even sharing just your chromosome synonyms file (chromosome.txt) may be enough to shed light on this issue. Please let me know if you are able to share any of your files, and if not, I will look into other ways to resolve your issue.

Thanks again,

Mason Meyer IGB Support Specialist

ADD COMMENTlink written 2.0 years ago by Mason Meyer110
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