Bowtie -n and -v mode

[ZhengXia]

Dear All,
When aligning long reads such as >75bp, which mode of Bowtie do you use? -n mode mapping the first L (default 28) bp of a read while -v mode maps the whole read allowing no more than v mismatch. I'm wondering which method is more suitable for the long read alignment.
Many thanks.

Best,

[SongLi]

As far as I know, quality accessment for long reads has not been done. It's still an open question for now.

Originally Posted by ZhengXia

Dear All,
When aligning long reads such as >75bp, which mode of Bowtie do you use? -n mode mapping the first L (default 28) bp of a read while -v mode maps the whole read allowing no more than v mismatch. I'm wondering which method is more suitable for the long read alignment.
Many thanks.

Best,

[xinwu]

Originally Posted by ZhengXia

Dear All,
When aligning long reads such as >75bp, which mode of Bowtie do you use? -n mode mapping the first L (default 28) bp of a read while -v mode maps the whole read allowing no more than v mismatch. I'm wondering which method is more suitable for the long read alignment.
Many thanks.

Best,

IMO, if you want to allow more number of mismatches, you can only use n mode with large e value, since both n or v option only allow at most 3 mismatches. Say, you can set -n 3 with larger e value.

[xinwu]

Originally Posted by SongLi

As far as I know, quality accessment for long reads has not been done. It's still an open question for now.

As manual said "read length can be 1024". Do you mean seq quality will be ignored when it is a long read? If so, what's the max length? Only n mode considering seq quality, will it affect v mode?