来自金史留青的邮件

[金史留青]

Dear UCSC Genome Bioinformatics Group：

        Thank you to give me some suggestions in the previous message mentioned and i would love to try any latent of possible in custom tracks. Adjunct is the  the GFF file that causes error.

        Thanks again!

Yours!

Shuai 

 

[Jairo Navarro Gonzalez]

Hello Shuai,

Thank you for your reply. It seems you forgot to send your GFF file that causes the error. Could you please resend the GFF file either directly to me or to the forum. It would also be helpful to know which organism and assembly version you are using at the Genome Browser.

I look forward to your reply. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro
UCSC Genomics Institute

 

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[Jairo Navarro Gonzalez]

Hello Shuai,

It appears that you are not using the UCSC Genome Browser, and instead you are using a mirror of the UCSC Genome Browser. The only mirror sites that we support are though this mailing-list are our official mirror sites:

• http://genome-euro.ucsc.edu/
• http://genome-asia.ucsc.edu/

However, after looking at your GFF file, there is an error with the first field of each line. For example, in the following line of your file: 

NC_000962.3    RefSeq    region    1    4411532    .    +    .    ID=id0;Dbxref=taxon:83332;gbkey=Src;genome=genomic;mol_type=genomic DNA;strain=H37Rv

The NC_000962.3 should be the chromosome name, such as chr:

chr    RefSeq    region    1    4411532    .    +    .    ID=id0;Dbxref=taxon:83332;gbkey=Src;genome=genomic;mol_type=genomic DNA;strain=H37Rv

Again, you are using a mirror of our site, and not the UCSC Genome Browser. Since this GFF file is for Mycobacterium tuberculosis, you may be using the Archaeal Genome Browser. Going to the Mycobacterium tuberculosis Genome Browser, it appears that this Genome Browser contains a Genbank RefSeq track that may interest you. If you are still experiencing errors when uploading your file to the Mycobacterium tuberculosis Genome Browser, please contact Todd Lowe at the Archaeal Genome Browser.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu.

All messages sent to that address are archived on a publicly-accessible Google Groups forum.
If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Jairo Navarro 
UCSC Genomics Institute

On Fri, Apr 21, 2017 at 9:20 PM, 金史留青 <sjss...@126.com> wrote:

Dear UCSC Genome Bioinformatics Group：

       I am very sorry that i forgot to put  the GFF file in adjunct so that hold up your time.This litter as an adddition in adjunct includes the GFF file.

      Thanks again!

 Yours!

Shuai