Comments (2)
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
from artic-ncov2019.
Great - thanks for the explanation and heads-up with the other repo!
from artic-ncov2019.
Related Issues (20)
- Conda environment dependency issues with new versions of Medaka
- nanopolish index -s failure / prime scheme download failure
- could not find primer scheme and reference sequence, attempting to download
- SARS-CoV-2
- Primer V5.3.2
- Installation via conda (different ways) failed HOT 1
- Artic enviroment does not install after 7 days HOT 2
- V4.1 scheme and primer BED file HOT 3
- Medaka failed: Command failed:longshot -P 0 -F -A --no_haps HOT 1
- multiple references in V4.1 refereces.fasta -> "FASTA has more than one sequence"
- Nanopolish error HOT 3
- Changing Minimum Sequencing Depth Parameter in artic-ncov2019 HOT 1
- Installing ARTIC stuck at Solving environment HOT 1
- artic assembly - Command failed:muscle -in & -out HOT 2
- Midnight primers scheme
- Update to V4/V4.1 under primer-schemes but not artic-ncov2019
- Error running artic minion
- align_trim ValueError: min() arg is an empty sequence (artic 1.2.1) HOT 1
- Error running nanopolish
- Help with vcf_merge HOT 1
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from artic-ncov2019.