Re: [Solexatools-users] Blat

[Brian O'C. <boc...@uc...>]

Hey Hanlee,

I haven't evaluated it yet but Dmitriy in our lab is taking a look and 
Ben Berman at UCS has been looking into it as well.  I've heard it's 
helpful because it takes into account the quality score as it does the 
alignment.  Dmitriy mentioned that it's similar to ELAND in that it 
doesn't allow for indels though. Are they adding support in the most 
recent version?  I wish I has seen his talk, do you know if anyone's 
going to post it online?

I'm cc'ing Ben and Dmitriy if they want to chime in.  I'll probably add 
wrappers for MAQ to solexa-pipeline soon.

--Brian

Hanlee Ji wrote:

>Hi Brian,
>
>Thanks for the information regarding BLAT.  I'm in DC for a sequencing meeting geared towards Solexa.
>
>Richard Durbin, one of the gurus at Sanger had any extensive talk about the MAQ tool in regards to InDels.  I seem to remember him mentioning that dealing with heterozygous InDels may be any issue.  Did you ever consider MAQ?
>
>Hanlee
>Sent via BlackBerry by AT&T
>  
>