Hi Felix,
I hope you are doing well! I reviewed some of the prior posts regarding 5-Base and wanted to echo what others have mentioned. Based on my understanding the DRAGEN pipeline does not have flags that will ignore methylation calls in M-Bias regions. This means that the data need to be trimmed, which is not good for cfDNA projects where methylation and fragmentomics features can be concurrently analyzed (this will reduce sequencing coverage, which is already lower). Beyond this, it seems that 5-Base data are locked behind DRAGEN, which really reduces accessibility. Although I imagine this would be challenging, it would be great if someone could develop pipelines that can process and analyze these data without using DRAGEN.
Update: I forgot to ask. Can I take the reference used for the DRAGEN processing and plug it into Bismark Methylation Extractor to make the methylation calls with our DRAGEN-processed data?
Updated 2 It does not work. Any ideas on how to take DRAGEN data and perform independent methylation calls?
Thank you,
Mike
Hi Felix,
I hope you are doing well! I reviewed some of the prior posts regarding 5-Base and wanted to echo what others have mentioned. Based on my understanding the DRAGEN pipeline does not have flags that will ignore methylation calls in M-Bias regions. This means that the data need to be trimmed, which is not good for cfDNA projects where methylation and fragmentomics features can be concurrently analyzed (this will reduce sequencing coverage, which is already lower). Beyond this, it seems that 5-Base data are locked behind DRAGEN, which really reduces accessibility. Although I imagine this would be challenging, it would be great if someone could develop pipelines that can process and analyze these data without using DRAGEN.
Update: I forgot to ask. Can I take the reference used for the DRAGEN processing and plug it into Bismark Methylation Extractor to make the methylation calls with our DRAGEN-processed data?
Updated 2 It does not work. Any ideas on how to take DRAGEN data and perform independent methylation calls?
Thank you,
Mike