I am trying to develop a workflow for performing differential expression analysis on long read direct RNA sequencing performed using the MinION from Oxford Nanopore Technology. The transcriptomics pipeline offered by ONT has a few bugs that still need to be worked out, so I am working out my own. Does anyone have any experience taking RNA-seq data from the MinION into DESEQ2 or a similar package? I started by using minimap2 (due to the fact that the parameters can be adjusted for nanopore technology) to generate a summarized experiment. I attempted to read in a table of metadata containing the list of fastq files and corresponding conditions into a data frame, but I received the error:
*tmp*, value = new("DataFrame", rownames = NULL, : nrow of supplied 'colData' must equal ncol of object
Perhaps I don't have the right understanding of what the metadata .csv file (I've also seen it referred to as a sample table) is supposed to look right. But that appears to be the one step that is preventing me from funneling my results into DESEQ2. If anyone has any advice or experience working with MinION data, I would really appreciate it.