Comments (3)
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
from wgbs-pipeline.
Hi Paul,
Thank you for your answer which is very helpful. I will try WGBS-pipeline
for my data.
Best regards
Qianhui
from wgbs-pipeline.
Glad to help. I'll close this issue, but please feel free to reopen if you have any further questions.
from wgbs-pipeline.
Related Issues (10)
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from wgbs-pipeline.