Allow bulge with bowtie

[StephaniePi83]

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 :

[FONT="Courier New"]
TAAAACATTCGCGTGTACTT-TGTACGCAG
||||||||||||||||||||-|||||||||
TAAAACATTCGCGTGTACTTATGTACGCAG[/FONT] (reference)

But with this command line, this reads doesn't align :

bowtie -v 3 -m 1 -a -t ref -c TAAAACATTCGCGTGTACTTTGTACGCAG

Is someone can help me to solve this problem ?

Thanks in advance,

[arvid]

Use a indel-capable aligner instead of Bowtie, popular choices include BWA, BFAST or Bowtie2 (but there are more). The original Bowtie wasn't designed for such alignments.

[StephaniePi83]

Ok thank you for your reply, i'll have a look on these tool