Align long nanopore minion cDNA reads

Question

[Nicolas Rosewick]

Hi,

I received some nanopore minion cDNA samples. My idea was to use STARlong to align them against my reference genome. Any other idea / advice to align such long reads containing a high error rate ; and taking into account splice junctions ..

Thanks

Answer 1

[mark.ziemann]

From the RNA-seq aligners I've tested, STAR was the most robust to mismatches, insertions and deletions (blog post).

That being said, I haven't yet tried lightweight mappers such as Kallisto for this task.