First time RNA-seq analyst here. I'm new to the ONT MinION platform, but not to R. I was wondering if anyone had experience using DESeq2 to analyze the long read, direct RNA sequencing results generated by the MinION. I have attempted to use minimap2 to align the reads (due to customized parameters that are specific to noisy long reads) , resulting in SAM/BAM files. I want to take them into DESeq2, which is favored by my colleagues. However, they use the more traditional sequencing platforms. I was able to read in the gene model and use summarizeOverlaps to count the reads. I was also able to generate a SummarizedExperiment, but from there I am a bit lost. The manual, (https://www.bioconductor.org/help/course-materials/2016/CSAMA/lab-3-rnaseq/rnaseqgeneCSAMA2016.html#preparing-count-matrices-from-bam-files), has references to a sample table that needs to be read in, but I'm not exactly sure what that means. The sample table must be assigned to the colData slot, "making sure that the rows correspond to the columns of the SummarizedExperiment".
If anyone has experience using ONT MinION reads with DESEQ2 (or another differential analysis package), I would appreciate any and all advice.