I have recently started working with RNA nonopore MinIon long reads. However, at the moment I have more doubts than answers.
From my (weak) understanding, there are 2/3 main approaches regardless to RNA nanopore miniIon:
- direct RNA
- direct cDNA (PCR-free)
- cDNA (with a PCR step)
The data that I have is from the direct cDNA (PCR-free protocol). And my doubts start here. From the nanopore website, it looks like this protocol generates 1D reads (so, reads with TTTTTTT at the start OR AAAAAAA at the ending). Can you confirm it? However, looking to my fastq-trimmed file, I have 2D reads, which means I have reads that start with TTTTTTT AND end with AAAAAAA. Does it be possible for direct cDNA protocol. If so, Can I conclude the strandness from these 2D data?
Thank you all in advance,