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artic-network / artic-ncov2019

ARTIC nanopore protocol for nCoV2019 novel coronavirus
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Invalid BED file column 5 #66

Closed nathanhaigh closed 3 years ago

nathanhaigh commented 3 years ago

Column 5 of the following BED files are not valid: nCoV-2019.scheme.bed and nCoV-2019.bed. Column 5 is supposed to be an integer score in the interval [0,1000]. As such, doing things like converting the file to BigBed format (using bedToBigBed) for visualisation in genome browsers fails for such files.

will-rowe commented 3 years ago

Hi @nathanhaigh

Yes, these don't conform to the BED standard. The *.scheme.bed files were actually replaced by *.primer.bed files in a later release of primal scheme, and these conform to BED standard (even though we hijack the 6th column for strand).

So try using the more recent version of the scheme files for your application. More details on our schemes are found in the artic primer scheme repo

nathanhaigh commented 3 years ago

Great - thanks for the explanation and heads-up with the other repo!