Searching names loading incorrect section in gbrowse

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Searching names loading incorrect section in gbrowse

John Portwood
Hello,

I'm having a problem with GBrowse2 (v 2.43) and the link to the archive mailing list wasn't working so I'm not able to see if this has been reported before. 

For only one track, when the name is searched in GBrowse the browser will navigate to a section that is slightly off from where the name is located. For example take this section from my GFF3 (rendered from grepping "GRMZM2G124745"):

Chr7    AGPv3   protein_coding_gene     176806695       176810119       .       +       .       Name=GRMZM2G124745;biotype=protein_coding;logic_name=genebuilder;ID=GRMZM2G124745
Chr7    AGPv3   transcript      176806695       176810119       .       +       .       Name=GRMZM2G124745_T01;Parent=GRMZM2G124745;biotype=protein_coding;description=est;logic_name=genebuilder;ID=GRMZM2G124745_T01
Chr7    AGPv3   exon    176806695       176806968       .       +       .       Name=GRMZM2G124745_E04;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;rank=1;ID=GRMZM2G124745_E04
Chr7    AGPv3   five_prime_UTR  176806695       176806706       .       +       .       Parent=GRMZM2G124745_T01;
Chr7    AGPv3   CDS     176806707       176806968       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=1;ID=GRMZM2G124745_P01
Chr7    AGPv3   CDS     176808089       176808340       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=2;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176808089       176808340       .       +       .       Name=GRMZM2G124745_E03;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=1;ensembl_phase=1;rank=2;ID=GRMZM2G124745_E03
Chr7    AGPv3   CDS     176808921       176809060       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=3;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176808921       176809060       .       +       .       Name=GRMZM2G124745_E01;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_phase=1;rank=3;ID=GRMZM2G124745_E01
Chr7    AGPv3   CDS     176810033       176810119       .       +       0       Name=GRMZM2G124745_P01;Parent=GRMZM2G124745_T01;rank=4;ID=GRMZM2G124745_P01
Chr7    AGPv3   exon    176810033       176810119       .       +       .       Name=GRMZM2G124745_E02;Parent=GRMZM2G124745_T01;constitutive=1;ensembl_end_phase=-1;rank=4;ID=GRMZM2G124745_E02

Searching for "GRMZM2G124745" in GBrowse will bring me to this region:
Chr7:176,822,753..176,826,177

However, on the first line in the above snippet you can see this element is actually located between 176,806,695 and 176,810,119 on Chr7. All of the elements are being rendered at their correct positions specified in the gff -- It's only when you search for them by name the browser takes you to a region ahead of them. 

This problem is not occurring with other tracks that I have loaded, so I'm guessing there's a problem either with the gff or the config file but after much research I'm still unable to find the cause of this issue.

Any help is greatly appreciated. Thanks!

-John 


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Re: Searching names loading incorrect section in gbrowse

John Portwood
This issue has been resolved. Thanks.



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