Which BS-seq analysis tool to choose?

[zeam]

I will do some analyses on BS-seq data(paired-end reads from Illumina).Is there anyone who have do the similar job like mine and could you give me some suggestions on choosing the BS-seq tools?
I have test BRAT,BSMAP,BISMARK,BS seeker.A paper in 2010 used BSMAP,but it's very slow.Could somebody give me some suggestions on choosing the BS-seq tools based on algorithms and accracy?
Thanks !

[fkrueger]

Hi Zeam,

it rather depends on your specific needs which tools you want to use. Some tools just do the mapping and you will have to figure out the methylation calls yourself, others such as BS_Seeker or Bismark will produce a very easy-to-mine methylation output.

I haven't tested BSMAP myself but according to the both the BRAT and the BS_Seeker papers it is indeed very slow (you mentioned this yourself), the other three tools (BS-Seeker, Bismark and BRAT) should be relatively comparable regarding their speed and possibly also their accuracy as they employ very similar approaches (I don't think BS-Seeker supports paired-end mapping though). So I guess you just choose the one you like best or which offers most flexibility for your specific application.