Use soft-masked or unmasked genome?

sinanugur / MirMachine

MirMachine, a command line tool to detect microRNA homologs in genome sequences.

https://mirmachine.readthedocs.io

MIT License

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Use soft-masked or unmasked genome? #16

Open cement-head opened 5 months ago

cement-head commented 5 months ago

Hello,

No mention of having to use soft-masked vs unmasked FASTA genome as input for MirMachine, so I assume that an unmasked genome is OK? Can you confirm? TIA

sinanugur commented 5 months ago

Hi,

It should not matter. I guess masked regions should not contain valid hits and MirMachine usually filters out low quality hits. However, it may slightly increase the runtime.

Cheers, @sinanugur