Where to get genome and annotation files

[smartgamer]

Hi,

I'm trying to use the RASflow and want to use the complete genome and annotation files(human). I tried to download files from https://uswest.ensembl.org/info/data/ftp/index.html, but don't know which files to download and fill the section for "Configuration for alignment to genome and feature count " in config_main.yaml. The original setting in the config_main.yaml is:

genome and annotation files

GENOME: data/example/ref/genome/Homo_sapiens.GRCh38.dna.chromosome.1.1.10M.fa ANNOTATION: data/example/ref/annotation/Homo_sapiens.GRCh38.93.1.1.10M.gtf

I want to replace these files with complete human genome files. Where can I download them and which files?

Thanks,

[kalavattam]

These links ought to do the trick.

# GENOME
ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/

# ANNOTATION
ftp://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens

[smartgamer]

Thank you so much

Charles

On Oct 25, 2020, at 10:54 PM, Kris Alavattam notifications@github.com wrote:



These links ought to do the trick.

GENOME

ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/

ANNOTATION

ftp://ftp.ensembl.org/pub/release-101/gtf/homo_sapiens

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[zhxiaokang]

Thank you @kalavattam