Reference genome masking

DaehwanKimLab / hisat2

Graph-based alignment (Hierarchical Graph FM index)

GNU General Public License v3.0

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Reference genome masking #182

Closed fbrundu closed 5 years ago

fbrundu commented 6 years ago

Hi, Which kind of reference genome should be provided to hisat2? Soft-masked or unmasked? I read the documentation on your website but I didn't find indication of which kind of masking to use on the genome.

Thanks for your work!

infphilo commented 5 years ago

Soft-masked sequences (lower-case sequences) in a reference is treated in the same way as upper-case sequences. If you wish to exclude some sequences for alignment, please replace them with Ns. We'll update the manual to include this information.

Best, Daehwan