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You will have to manually edit the cigar strings. It's possible that if you align to the reverse-complement of the reference, the deletion will be put in the alternate location, though.
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Originally posted by Brian Bushnell View PostPerhaps I'm confused, but it looks like there are 3 classes of reads:
TACTCAAAGG (normal)
TACCCGAAGG (mutant 1)
TACCCGAGG (mutant 2)
The second class of mutant has a deletion in it, so of course it has to be aligned with a deletion somewhere.
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Perhaps I'm confused, but it looks like there are 3 classes of reads:
TACTCAAAGG (normal)
TACCCGAAGG (mutant 1)
TACCCGAGG (mutant 2)
The second class of mutant has a deletion in it, so of course it has to be aligned with a deletion somewhere.
Leave a comment:
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Alignment with BWA
Hello!
Im using this BWA to align some reads
Code:bwa index -p my_reference my_reference.fasta bwa mem -t 4 my_reference input.fastq > output.sam 2
Attached FilesTags: None
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