Dear all:
For some reasons, I need align my short read sequence as following conditions:
refseq: ATCCGATTGCCTCCAAATGCCCTAAATCGTA
my_sq: ATCC-AT-GCCTC-AAATGCCC-AAA-CG-A
(1) for the first 18 nt (red colored) from 5':
a. set as a seed
b. allow 3 mismatches (shown as red "-")
(2) Allow total 6 mismatches (rest mismatches as blue "-")
I tried to find some aligners, but I cannot find a good one.
For example, if I use bowtie with -n and allow 3 mismatch on seed, i cannot set the parameters for total 6 mismatches allowed.
Do you have any suggestions? Thanks a lot!!
Best,
Yi
For some reasons, I need align my short read sequence as following conditions:
refseq: ATCCGATTGCCTCCAAATGCCCTAAATCGTA
my_sq: ATCC-AT-GCCTC-AAATGCCC-AAA-CG-A
(1) for the first 18 nt (red colored) from 5':
a. set as a seed
b. allow 3 mismatches (shown as red "-")
(2) Allow total 6 mismatches (rest mismatches as blue "-")
I tried to find some aligners, but I cannot find a good one.
For example, if I use bowtie with -n and allow 3 mismatch on seed, i cannot set the parameters for total 6 mismatches allowed.
Do you have any suggestions? Thanks a lot!!
Best,
Yi
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