Re: [MUMmer-help] SNP detection with fasta files containing more than one sequence?

[Adam P. <ada...@ya...>]

Hi Aaron,
Multiple fasta records are allowed in both the reference and query files. You are probably experiencing some "sequence uniqueness" complications. Try adding the --maxmatch option to the nucmer invocation, and things should start working for you. See:

http://mummer.sourceforge.net/manual/#mummer

for a *very* brief explanation of what the different uniqueness settings mean (mum, mumereference, maxmatch). Basically, if the same exact sequence is repeated multiple times in your reference file (or query file) it will be filtered from the output by default. If you turn on the --maxmatch flag and still have problems, get back to me.

Best, 
Adam

Aaron Gussman <agu...@ti...> wrote: Can there be multiple fasta records in either the reference or query 
fasta file passed to nucmer?  I was following the steps in section "4.4 
SNP detection" of the FAQ, but no snps are detected if I include more 
than one fasta record in the reference or query file.  However, 1:1 
comparisons do produce show-snps output.  Section 3 of the FAQ says that 
the reference and query files can contain any number of sequences, so 
I'm puzzled as to what's going on.

I've included the test sequences I was trying below.  Any help is 
appreciated.

Thanks,
Aaron

 >QUERY_01 01
ATGACCCAAACCGAAATGTAGATGAAAATGCTAATGCCAACAATGCTGTAAAAAATAATAATAACGAAGAGCCAAGTGATCAGCACATAGAAAAATATTTAAAGAGAATACAAAATTCTCTTTCAACTGAATGGTCCCCATGTAGTGTAACTTGTGGAAATGGTATTCAAGTTAGAATAAAGCCTGGCTCTGCTAATAAACCTAAAGACCAATTAGATTATGCAAATGATATTGAAAAAAAAATTTGTAAAATGGAAAAATGTTCCAGTGTGTTTAATGTCGTAAATA

 >REFERENCE_02 02
ATGACCCAAACCGAAATGTAGATGAAAATGCTAATGCCAACAATGCTGTAAAAAATAATAATAACGAAGAACCAAGTGATCAGCACATAGAAAAATATTTAAAGAGAATACAAAATTCTCTTTCAACTGAATGGTCCCCATGTAGTGTAACTTGTGGAAATGGTATTCAAGTTAGAATAAAGCCTGGCTCTGCTAATAAACCTAGAGACCAATTAGATTATGCAAATGATATTGAAAAAAAAATTTGTAAAATGGAAAAATGTTCCAGTGTGTTTAATGTCGTAAATA
 >REFERENCE_03 03
TATTTACGACATTAAACACACTGGAACATTTTTCCATTTTACAAATTTTTTTTTCAATATCATTTGCATAATCTAATTGGTCTTTAGGTTTATTAGCAGAGCCAGGCTTTATTCTAACTTGAATACCATTTCCACAAGTTACACTACATGGGGACCATTCAGTTGAAAGAGAATTTTTTATTTTGTTTAAATATTTTTCTATGTGCTGATCACTTGGTTCTTCGTTATTATTATTTTTTACAGCATTGTTGGCATTAGCATTTTCATCTACATTTCGGTTTGGGTCA



-- 
Aaron Gussman - Bioinformatics Engineer I
The Institute for Genomic Research
agu...@ti...
(301) 795-7698


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