1 hour ago by
United States
The file you are looking for is feature_table.txt.gz located in the same FTP directory where the genome FASTA, assembly report, GPFF, etc are located. For example, this is FTP path for the Salmonella assembly: ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/006/945/GCF_000006945.2_ASM694v2 and you can find the feature_table.txt file in that directory. This is a tab-delimited file with information about all of the features annotated on the genome. Specifically, you can get the range of genes using something along the lines of:
zcat GCF_000006945.2_ASM694v2_feature_table.txt.gz
| awk 'BEGIN{FS="t";OFS="t"}($1~/^#/ || $1=="gene"){print $7,$8,$9,$10,$15,$16,$17}'
genomic_accession start end strand symbol GeneID locus_tag
NC_003197.2 190 255 + thrL 1251519 STM0001
NC_003197.2 325 2799 + thrA 1251520 STM0002
NC_003197.2 2789 3730 + thrB 1251521 STM0003
NC_003197.2 3722 5020 + thrC 1251522 STM0004
Note, the coordinates in this table are 1-based and you should subtract 1 from the start position if you want to use bedtools for any downstream steps.
