Align long nanopore minion cDNA reads
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7.3 years ago

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 • 2.1k views
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Entering edit mode
7.3 years ago
mark.ziemann ★ 1.7k

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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