Hi everybody,
I was wondering if it is possible to allow a bulge with bowtie.
for example, i have reads which map to the reference like that :
But with this command line, this reads doesn't align :
Is someone can help me to solve this problem ?
Thanks in advance,
I was wondering if it is possible to allow a bulge with bowtie.
for example, i have reads which map to the reference like that :
Code:
[FONT="Courier New"] TAAAACATTCGCGTGTACTT-TGTACGCAG ||||||||||||||||||||-||||||||| TAAAACATTCGCGTGTACTTATGTACGCAG[/FONT] (reference)
Code:
bowtie -v 3 -m 1 -a -t ref -c TAAAACATTCGCGTGTACTTTGTACGCAG
Thanks in advance,
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