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lhqing / cemba_data

Mapping pipeline for snmC-seq based technologies.
https://hq-1.gitbook.io/mc/
MIT License
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outdated manual at https://hq-1.gitbook.io/mc #19

Open mbatiuk opened 5 months ago

mbatiuk commented 5 months ago

manual is outdated at https://hq-1.gitbook.io/mc

Such as there is no mentioning about alternative to bismark hisat3n in the reference section: https://hq-1.gitbook.io/mc/prepare/prepare-mapping-config/prepare-reference-files

However hisat3n is an option in the parameters for yap default-mapping-config

--hisat3n_dna_ref HISAT3N_DNA_REF Path to the hisat-3n DNA reference (default: None) --hisat3n_rna_ref HISAT3N_RNA_REF Path to the hisat-3n RNA reference (default: None)

Github env.yaml also mentions more up to date packages for environment setup than guidline on https://hq-1.gitbook.io/mc/installation, as well as alternative environment hisat3n_env.yml