Align long nanopore minion cDNA reads

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

nanopore alignment long-reads

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updated 3.9 years ago by Ram

• written 11.0 years ago by Nicolas Rosewick

1 answer

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.

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updated 3.9 years ago by Ram

• written 11.0 years ago by mark.ziemann

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