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  • fibar
    Member
    • Feb 2013
    • 19

    #1

    Count BLAST hits and 'no hits'

    I'm performing local blastn.
    My query file consists in 20 sequences, and I have my own databases (DB) created out of several short reads Illumina files.

    I ran the blastn (with e values > 1e-04) against each DB and need to output an 'abundance-like' table, showing the hits (including 0 hits) for each database file.

    Example:
    DB1 DB3 DB4 ...
    seq1 2 4 7
    seq2 1 0 8
    seq3 8 9 6
    ...

    Again: Here, the numbers represent the hits for each query sequence in each database.

    Does anyone know a possible way to get this?
  • maubp
    Peter (Biopython etc)
    • Jul 2009
    • 1544

    #2
    Have you learnt to program yet? This should only need a short Perl, Python or Ruby script (or some other language - find out what your local experts use so you can have some in person mentoring)

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