Closed vineetbansal closed 1 year ago
There are 2 formats for files that give the mapping between "common names" for chromosomes and their accession numbers.
The chr2acc format that we're supporting now, e.g.: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_assembly_structure/Primary_Assembly/assembled_chromosomes/chr2acc
chr2acc
#Chromosome Accession.version I NC_001133.9 II NC_001134.8 III NC_001135.5 IV NC_001136.10
and the *.chromAlias.txt format, e.g. https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chromAlias.txt
*.chromAlias.txt
# ucsc genbank refseq assembly ncbi chr1 CP068277.2 NC_060925.1 1 1 chr10 CP068268.2 NC_060934.1 10 10 chr11 CP068267.2 NC_060935.1 11 11 chr12 CP068266.2 NC_060936.1 12 12
We'll need to modify our add-organism command to play well with the latter.
add-organism
There are 2 formats for files that give the mapping between "common names" for chromosomes and their accession numbers.
The
chr2acc
format that we're supporting now, e.g.: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/146/045/GCF_000146045.2_R64/GCF_000146045.2_R64_assembly_structure/Primary_Assembly/assembled_chromosomes/chr2accand the
*.chromAlias.txt
format, e.g. https://hgdownload.soe.ucsc.edu/goldenPath/hs1/bigZips/hs1.chromAlias.txtWe'll need to modify our
add-organism
command to play well with the latter.