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I am using higlass 1.7.2 and I am having issues with uploading bigwigs with specified chromosome sizes. I have tried specifying the uuid, name, and file of the two different chromosome sizes that are there when I use list_tilesets. I get the error that the coordinate system does not match the specified coordinate system (below). I have tried created bigwigs using the method you provided for converting bedgraphs to bigwigs.
If I do not specify a coordSystem the file uploads but I have had issues with the coordinates being slightly off. I would like to be able to specify the chromosome sizes so I know before looking at data whether the bigwig is not constructed with the correct chromosome sizes. How do I fix this issue? Is there a public chromosome sizes that higlass is finding that would not show up when listing tilesets since it ingests the bigwig if I do not specify chromosome sizes?
Error when I try to supply chromosome sizes:
CommandError: Matching chromosome sizes (coordSystem: {}) do not match the specified coordinate sytem ({}). Either omit the coordSystem or specify a matching one.See http://docs.higlass.io/data_preparation.html#bigwig-files for more information
Warning when I do not supply chromosome sizes:
No coordinate system specified, but we found matching chromsizes. Using coordinate system .
The text was updated successfully, but these errors were encountered:
I am using higlass 1.7.2 and I am having issues with uploading bigwigs with specified chromosome sizes. I have tried specifying the uuid, name, and file of the two different chromosome sizes that are there when I use list_tilesets. I get the error that the coordinate system does not match the specified coordinate system (below). I have tried created bigwigs using the method you provided for converting bedgraphs to bigwigs.
If I do not specify a coordSystem the file uploads but I have had issues with the coordinates being slightly off. I would like to be able to specify the chromosome sizes so I know before looking at data whether the bigwig is not constructed with the correct chromosome sizes. How do I fix this issue? Is there a public chromosome sizes that higlass is finding that would not show up when listing tilesets since it ingests the bigwig if I do not specify chromosome sizes?
Example code: ./manage.py ingest_tileset --filename test.bw --filetype bigwig --coordSystem Homo_sapiens_assembly38.chrom.sizes --uid test_cov_bw
Error when I try to supply chromosome sizes:
CommandError: Matching chromosome sizes (coordSystem: {}) do not match the specified coordinate sytem ({}). Either omit the coordSystem or specify a matching one.See http://docs.higlass.io/data_preparation.html#bigwig-files for more information
Warning when I do not supply chromosome sizes:
No coordinate system specified, but we found matching chromsizes. Using coordinate system .
The text was updated successfully, but these errors were encountered: