I have made a local NCBI database on my computer, and it works. I am now trying to extract sequences from the database after i blast it. I am using bedtools version 2.26 and trying to use the getfasta command. The issue is when i run it I get : The requested fasta database file (C:UsersOwnerDesktopLocalDBdatabase.fasta) could not be opened. Exiting! I am on a windows computer and using Bash on Ubuntu as the terminal.
$ bedtools getfasta -fo test -tab -fi C:\Users\Owner\Desktop\LocalDB\database.fasta -bed C:\Users\Owner\Desktop\LocalDB\Book1.txt
is the original command I inputted. I have a bed file of Book1 but i heard it will read txt files just fine. but for now the issue is reading the database. Thanks!!!