Nanopore bioinformatics & EPI2ME

AnMa21 · 11-10-2021, 12:23 AM

Hello! I've just started a PhD in DNA sequencing for the identification of cancer biomarkers and I was hoping to get some advice on bioinformatic methods. Part of my experimental design is to carry out Nanopore sequencing and I'm quite new to long-read sequencing and bioinformatics. I'd originally planned to use the 'easy' bioinformatic pipeline as advertised by Nanopore so I could practice/learn command line but not miss out on sequencing samples, however I've also noticed its not common to see it in journals or discussions.

Why is this? Would I be unable to publish data analysed with epi2me? Is it better if I sequence the samples THEN carry out bioinformatic analysis when I'm more confident in it?

Thanks!!

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11-10-2021, 12:23 AM	#1
AnMa21 Junior Member Location: Edinburgh, UK Join Date: Nov 2021 Posts: 1	Nanopore bioinformatics & EPI2ME Hello! I've just started a PhD in DNA sequencing for the identification of cancer biomarkers and I was hoping to get some advice on bioinformatic methods. Part of my experimental design is to carry out Nanopore sequencing and I'm quite new to long-read sequencing and bioinformatics. I'd originally planned to use the 'easy' bioinformatic pipeline as advertised by Nanopore so I could practice/learn command line but not miss out on sequencing samples, however I've also noticed its not common to see it in journals or discussions. Why is this? Would I be unable to publish data analysed with epi2me? Is it better if I sequence the samples THEN carry out bioinformatic analysis when I'm more confident in it? Thanks!!