How to export methylation tracks in bed format
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Federica ▴ 10
@federica-24874
Last seen 16 months ago
Italy

Hi,

I am doing analysis of methylation data from EPIC array (Illumina). After running analysis with RnBeads, the analysis.log file reports warning messages concerning the tracks and tables module, as reported following:

STATUS             STARTED Exporting sites
2021-03-07 15:36:10     2.6  STATUS                 STARTED Creating Track Hub -- bigBed
2021-03-07 15:36:10     2.6 WARNING                     Skipped conversion bed -> bigBed for region type sites; could not find the tool bedToBigBed
2021-03-07 15:36:10     2.6  STATUS                 COMPLETED Creating Track Hub -- bigBed
2021-03-07 15:36:11     2.6  STATUS                 STARTED Creating UCSC Track Hub -- bigWig
2021-03-07 15:36:11     2.6 WARNING                     Skipped conversion bedGraph -> bigWig for region type sites; could not find the tool bedGraphToBigWig
2021-03-07 15:36:11     2.6  STATUS                 COMPLETED Creating UCSC Track Hub -- bigWig
2021-03-07 15:36:11     2.6  STATUS             COMPLETED Exporting sites

How could I solve the skipped conversion to bigBed and bigWig? The warning says that there aren't bedToBigBed bedGraphToBigWig tools... are they R packages?

Thank u!

RnBeads • 350 views
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@james-w-macdonald-5106
Last seen 5 hours ago
United States

Presumably what is required are various tools from Jim Kent at UCSC. I don't see anything in the README for that package or in the dependencies that say you need those things, but then I didn't really look that closely either.

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