Previously, I have done illumina data analysis so have experience in doing that. However, Nanopore is bit new to me and I am quite confused in its data analysis. I have epi2me (I guess it uses centrifuge) analysed data but I want to do reclassification using other database. Should I use basecalled data or epi2me data for further analysis? What if I convert those file format in biom format and then proceed with different R packages (as I have already done it). Is it possible to convert fast5 or fastq files in biom format? Can anyone suggest me steps or pipeline so that I can analyse my nanopore data. The whole idea is to interlink Nanopore resources with R packages and then carry out analysis.
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