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Unable to Match Data in this Source with Reference

asked 2017-10-30 17:35:39 -0600

Brian Davis (2) gravatar image

I am examining Illumina data aligned to a scaffold-level genome (30,000 contigs). I can browse these BAMs in other genome viewers (like IGV), but my preference is GenomeBrowse for numerous reasons. I have converted the very same genome fasta to GB's format, but unlike the dozen or so other species I have examined using GenomeBrowse, the indexed BAM files will not load. I receive "Unable to match data in this source with an existing reference sequence. Reference sequence must have matching chromosome names and lengths." I have validated that the names are the same (even though it's the exact same file) - they are based on NCBI accessions, and that lengths correlate to the correct contig. Is this a known problem?

Thank you in advance, -Brian

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answered 2017-11-09 15:17:39 -0600

SteveHystad gravatar image

Hi Brian,

This sounds like there is a discrepancy between the headers in your BAM file and the names of the scaffolds in the assembly file that is created when converting your genome fasta in GB. You could check by plotting the BAM in GB and under the console window, examining the coordinates in the BAM file.

Then compare these coordinates to what is found in the assembly file. This is typically found in your user data folder. To access this folder from GenomeBrowse, you can click tools > Open Folder > Annotations folder. Then back-up one directory to find the Assemblies folder. you can open the assemblies file in a text editor and change the order of the chromosomes.

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Asked: 2017-10-30 17:35:39 -0600

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Last updated: Nov 09 '17