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alexdobin / STAR

RNA-seq aligner
MIT License
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Specific mismatches #1244

Open ezecalvo opened 3 years ago

ezecalvo commented 3 years ago

Hi,

I was wondering if there's a way to allow for specific mismatches when using STAR. For example, can I set my run so it doesn't score a G>A substitution in any position?

Thanks!

alexdobin commented 3 years ago

Hi @ezecalvo

this is not possible - and it's not easy to implement. The best option is to reduce the alphabet like it's done for bisulfite sequencing.

Cheers Alex

ezecalvo commented 3 years ago

Got it, thanks!

Can STAR map using IUPAC notation in the reference genome?