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  • ashkot
    replied
    Update

    Thanks, a lot, BLAST is working now. It had to do with the database being not available in the right format.

    Leave a comment:


  • maubp
    replied
    Originally posted by ashkot View Post
    Right, so i used makeblastdb as follows

    makeblastdb -in human_g1k_v37.fasta -title human_g1k_v37

    it made three files each with
    .psq, .phr and .pin file extensions
    From the extensions that made a protein database (which is the default behaviour IIRC). There is an option to makeblastdb to make a nucleotide database which you'll need to use.

    Leave a comment:


  • ashkot
    replied
    Files and still getting error

    Right, so i used makeblastdb as follows

    makeblastdb -in human_g1k_v37.fasta -title human_g1k_v37

    it made three files each with
    .psq, .phr and .pin file extensions

    i am trying to execute blastn as follows

    blasntn -query {query file} -db human_g1k_v37 -out Results.txt -strand plus

    I am getting error 'No index or alias found for database human_g1k_v37'

    thanks

    Leave a comment:


  • maubp
    replied
    What files did formatdb create? And why are you using formatdb - that's from legacy BLAST, you should be using makeblastdb for BLAST+

    Leave a comment:


  • ashkot
    replied
    Follow up info

    Thanks for link to that article.

    I am using blast-2.2.25+ on Ubuntu and formatdb -n human_g1k_v37_fasta.fasta

    The exact error i get when i try to run blastn is index file not found for database human_g1k_v37_fasta

    Thanks.

    Ashwin

    Leave a comment:


  • maubp
    replied
    In principle there is no reason why human_g1k_v37_fasta cant be used as a BLAST database.

    I suggest reading this: Ten Simple Rules for Getting Help from Online Scientific Communities


    For a start, which version of BLAST are you using, which OS are you using, and what were the commands you ran to build the database, and to execute the BLAST search, and what was the EXACT error message?

    Leave a comment:


  • ashkot
    started a topic FASTA database of human_g1k_v37.fasta

    FASTA database of human_g1k_v37.fasta

    Hi all,
    I want to BLAST using the human_g1k_v37_fasta as database. When i run formatdb on this file and run blast subsequent to that, i get a message stating index file not found.

    Can someone please let me know if it's possible to convert this file to FASTA database and if so the command to be used.

    Thanks in advance.

    Ashwin

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