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docs: update BED format
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deliaBlue committed Jan 25, 2024
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9 changes: 5 additions & 4 deletions config/README.md
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Expand Up @@ -100,10 +100,10 @@ There are 4 files you must provide:
resource][chrMap] provides such files for various organisms, and in the
expected format.

5. **OPTIONAL**. ASCII-style pileups of read alignments produced for individual
libraries, combinations of libraries and/or all libraries of a given run.
The exact number and nature of the outputs depends on the workflow
inputs/parameters.
5. **OPTIONAL**: A **BED6** file with regions for which to produce
[ASCII-style alignment pileups][ascii-pileups] for. If not provided, no
pileups will be generated. Refer [here][bed-format] to see the expected
format.

> General note: If you want to process the genome resources before use (e.g.,
> filtering), you can do that, but make sure the formats of any modified
Expand All @@ -124,6 +124,7 @@ parameters to your liking. The template explains what each of the parameters
mean and how you can meaningfully adjust them.

[ascii-pileups]: <https://git.scicore.unibas.ch/zavolan_group/tools/ascii-alignment-pileup>
[bed-format]: <https://gist.github.com/deliaBlue/19ad3740c95937378bd9281bd9d1bc72>
[chrMap]: <https://github.com/dpryan79/ChromosomeMappings>
[ensembl]: <https://ensembl.org/>
[ensembl-bed]: <https://www.ensembl.org/info/website/upload/bed.html>
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