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FelixKrueger / SNPsplit

Allele-specific alignment sorting
http://felixkrueger.github.io/SNPsplit/
GNU General Public License v3.0
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Using the --full_sequence genome #51

Closed ezecalvo closed 2 years ago

ezecalvo commented 2 years ago

Hi,

I created a hybrid genome using the --full_sequence option to avoid masking and get a higher mapping accuracy. Nevertheless, 100% of my reads are unassignable after mapping because there are no Ns, which makes perfect sense.

What's the point of having the --full_sequence option if you can't split reads to alleles after? Is it just a SNPsplit feature to create a new genome?

Thanks!

FelixKrueger commented 2 years ago

Indeed, it is just to create new genomes (sometimes you might want to extract FastA sequences and look at them side-by-side); it is also required as the new reference genome in case you are generating dual strain hybrids.

ezecalvo commented 2 years ago

Got it, thanks!