Question: Align long nanopore minion cDNA reads
gravatar for Nicolas Rosewick
5.0 years ago by
Belgium, Brussels
Nicolas Rosewick9.0k wrote:


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


nanopore long reads alignment • 1.6k views
ADD COMMENTlink modified 5.0 years ago by mark.ziemann1.2k • written 5.0 years ago by Nicolas Rosewick9.0k
gravatar for mark.ziemann
5.0 years ago by
mark.ziemann1.2k wrote:

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.


ADD COMMENTlink written 5.0 years ago by mark.ziemann1.2k
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