Tool:Batmeth: Improved Mapper For Bisulfite Sequencing Reads On Dna Methylation

Question

[brentp]

This looks to be a very impressive tool for mapping BS-Seq data in base-space and colorspace. http://genomebiology.com/2012/13/10/R82

Figure 2 shows a comparison with some other aligners: http://genomebiology.com/2012/13/10/R82/figure/F2

BatMeth has a lower false+ rate with good speed and good true+

They evaluate on real data in base and colorspace, and on simulated data (and it's not their own simulator).

The method is outlined in figure 4: http://genomebiology.com/2012/13/10/R82/figure/F4

Briefly the process for a single read is:

1. convert reference for + and -
2. convert read for + and -
3. check 4 possible mappings of read
4. exclude read if it maps to > N possible locations
5. compute number of mismatches and report its status as unique or not (only unique reads are used in calculation).

Since this is similar or identical to other BS-Seq mappers, it's not clear to me where they gain in accuracy. It must be that

1. They discard low-complexity reads (based on shannon-entropy).
2. They discard reads that are not unique

[Istvan Albert]

on an unrelated note it seems these bisulfite mappers have the strangest names: BS Seeker, BatMeth, BS Map

[brentp]

when I first wrote MethylCoder, it spent a few days as "MethLab"

[Istvan Albert]

hehe, for a second I imaged what it would sound like to ask for funding to "improve the MethLab run times"