A question about the differences between wgbs-pipeline and dna-me-pipeline

[QianhuiWan]

Hello, I found dna-me-pipeline and wgbs-pipeline from ENCODE, what are the differences between these 2 pipelines in terms of analysing WGBS data? Thank you so much! Best regards, Qianhui

[paul-sud]

Hi Qianhui,

dna-me-pipeline is older and only runs on DNAnexus. It was used to process ENCODE data some time ago. That pipeline uses Bowtie2 for alignment and Bismark for methylation calls, among other software. You can find a high-level schematic here: https://www.encodeproject.org/pipelines/ENCPL985BLO/

wgbs-pipeline is newer and will be used to process ENCODE data going forward. It is based on WDL and can run on multiple platforms. It uses gemBS for alignment and methylation calling and also includes smoothing of CpG methylation values via Bsmooth.

I hope that helps, please let me know if you have any additional questions.

Best,

Paul

[QianhuiWan]

Hi Paul,

Thank you for your answer which is very helpful. I will try WGBS-pipeline for my data.

Best regards
Qianhui

[paul-sud]

Glad to help. I'll close this issue, but please feel free to reopen if you have any further questions.