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Mapping target bisulfite sequencing reads to a reference

Hi,

I'm looking for software to map the sequencing reads from bisulfite treated synthetic DNA to a reference sequence. What I'm interested to get is the alignment to the reference, since I need to process the data further to extract preferred methylation sites.Do you know any software that would be suitable for this?

Thanks a lot in advance,
Tomek

bisulfite-seq next-gen-sequencing alignment
• 2,849 views • link
updated by Ram Ram • written by tomasz.jurkowski • tomasz.jurkowski

3 answers

ttp://lmgtfy.com/?q=mapping+genome+bisulphyte

segemehl if working with CpG

Bismark if working with CpG and non canonical methylations as in plant CHH CHG

BSMAP

Some more are available, but these are popular

• 1 views • link
updated by Ram Ram • written by Antonio R. Franco Antonio R. Franco

http://www.bioinformatics.babraham.ac.uk/projects/bismark/

• 1 views • link
updated by Ram Ram • written by dora dora
QuasR library in R. The alignment portion in both QuasR and Bismark is actually performed by Bowtie.
• 1 views • link
written by jomo018 jomo018

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