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igvteam / igv.js

Embeddable genomic visualization component based on the Integrative Genomics Viewer
MIT License
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Adding support for bedmethyl files #1696

Closed Ge0rges closed 6 months ago

Ge0rges commented 1 year ago

Bedmethyl files containing DNA methylation information are a defined standard that are becoming more widely used. Nanopore's cheap sequencing technology is making methylation data more accessible every year, and significant resources have been spent producing quality tools to interpret that data. The standard nanopore tool modkit has embraced the bedmethyl standard (and so have many other tools).

It would be nice if IGV supported bedmethyl files out of the box.

jrobinso commented 1 year ago

If the bed file has space delimited columns it will not work currently, however the bigBed version should work. Could you be more specific about this request, and include sample test files (bed and bigBed forms).

Also, I'm going to transfer this to igv.js as that is where any fixes will be done.

jrobinso commented 1 year ago

BTW these files work if you fix the tabs. This from the data you posted in the other issue.

https://tinyurl.com/254u2vb7

Bigbed would work much better (faster), and the extra columns could be used if you define the autosql. Bed doesn't really have a structure for defining extra columns.

Ge0rges commented 1 year ago

Sounds like you support bedmethyl files when they are in TSV format (which we argue here should be the default). If that's the case I consider this issue closed. I leave it to you to determine if added compatibility is required.

Please let me know if I can be of any help, looks like you have example data from the previous issue. Happy to provide any more needed.

jrobinso commented 1 year ago

@Ge0rges we could take advantage of those 2 extra columns by adding a ".bedmethyl" extension as a new format. We would just show them in the popup text. I'm happy to do that, but if you load a tab delimited file with ".bed" extension it should just work. Bigbed files should have autosql defining all the columns, so for that format a new extension is not needed.

jrobinso commented 1 year ago

I'm going to reopen as a reminder to myself to add the extension

jrobinso commented 1 year ago

The extension has been added, so igv will know what to do with ".bedmeythl" files. ".bed" will still work, but you won't get the last 2 columns in popup text. This will be part of the next release, which will be sometime in October.