getfasta won't read my database
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!!!
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WouterDeCoster
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Justin.kallman •
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If it is an NCBI blast+ database I don't think bedtools is going to work. Are you trying to retrieve sequences for intervals in a bed file? You will need to use
blastdbcmdcommand to retrieve fasta sequences you want from the blast database into a new file. Once you have them in a new set, you can usebedtools getfastato get intervals you need.So i was toying around with it and I found the first problem which is Ubuntu doesn't read with backslashes and I have to add /mnt/ before i go into anyfiles. I now get index file /mnt/c/Users/Owner/Desktop/LocalDB/database.fasta.fai not found, generating...
The idea is that I blast a sequence against my database and I pull out all the sequences that match it for downstream analysis. Can i use blast command to do that?
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