If I have a reference sequence:
>reference
CTAGAATATCACTTAGGCCGGTATTCTATTACTGTACTTCGCGTAAGCTGCTTTAACCC
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GCAAGATTCGCGTGACCCCCACATCCTGGTTCTTCACGAGCAAAGTGTCCTTGCAAATA
and two query sequences (in a multifasta file):
>query1
CTAGAATATCACTTAGGCCGGTATTCTATTACTGTACTTCGCGTAAGCTGCTTTAACCC
>query2
GCAAGATTCGCGTGACCCCCACATCCTGGTTCTTCACGAGCAAAGTGTCCTTGCAAATA
bowtie2 will correctly map the two query sequences onto the reference.
However, if I change the query to exactly match the reference:
>query
CTAGAATATCACTTAGGCCGGTATTCTATTACTGTACTTCGCGTAAGCTGCTTTAACCC
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GCAAGATTCGCGTGACCCCCACATCCTGGTTCTTCACGAGCAAAGTGTCCTTGCAAATA
the query does not map (at all) to the reference.
The command line parameters are:
bowtie2 --sensitive-local -x reference.fa -f -U query.fa -S output.sam
Can anyone explain why this occurs?
>reference
CTAGAATATCACTTAGGCCGGTATTCTATTACTGTACTTCGCGTAAGCTGCTTTAACCC
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GCAAGATTCGCGTGACCCCCACATCCTGGTTCTTCACGAGCAAAGTGTCCTTGCAAATA
and two query sequences (in a multifasta file):
>query1
CTAGAATATCACTTAGGCCGGTATTCTATTACTGTACTTCGCGTAAGCTGCTTTAACCC
>query2
GCAAGATTCGCGTGACCCCCACATCCTGGTTCTTCACGAGCAAAGTGTCCTTGCAAATA
bowtie2 will correctly map the two query sequences onto the reference.
However, if I change the query to exactly match the reference:
>query
CTAGAATATCACTTAGGCCGGTATTCTATTACTGTACTTCGCGTAAGCTGCTTTAACCC
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
GCAAGATTCGCGTGACCCCCACATCCTGGTTCTTCACGAGCAAAGTGTCCTTGCAAATA
the query does not map (at all) to the reference.
The command line parameters are:
bowtie2 --sensitive-local -x reference.fa -f -U query.fa -S output.sam
Can anyone explain why this occurs?
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