Cats

[mr-eyes]

https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_018350175.1/

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/350/175/GCF_018350175.1_F.catus_Fca126_mat1.0/GCF_018350175.1_F.catus_Fca126_mat1.0_genomic.fna.gz

snipe sketch --ref GCF_018350175.1_F.catus_Fca126_mat1.0_genomic.fna.gz  -k 51 --scale 10000 -n fcatus_fca126_mat1_k51_s10k -o fcatus_fca126_mat1_k51_s10k.zip

Sketching genome with ksize=51, scale=10000, cores=4
Autodetected chromosomes:
autosome-a2	autosome-a1	autosome-a3	autosome-b2	autosome-b3	autosome-b1	
autosome-b4	autosome-d1	autosome-c2	autosome-d2	autosome-c1	autosome-d3	
autosome-e1	autosome-d4	autosome-e2	autosome-e3	mitochondrial-M	autosome-f1	
autosome-f2	sex-x	
Autosomal chromosomes: 18, Sex chromosomes: 1, Mitochondrial: 1
Sketching completed in 16.78 seconds.

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/350/175/GCF_018350175.1_F.catus_Fca126_mat1.0/GCF_018350175.1_F.catus_Fca126_mat1.0_rna.fna.gz

snipe sketch --amplicon GCF_018350175.1_F.catus_Fca126_mat1.0_rna.fna.gz -c 8 -n rna_fcatus_fca126_mat1_k51_s10k -o rna_fcatus_fca126_mat1_k51_s10k.zip

wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/018/350/175/GCF_018350175.1_F.catus_Fca126_mat1.0/GCF_018350175.1_F.catus_Fca126_mat1.0_genomic.gff.gz

bash extract_exome.sh GCF_018350175.1_F.catus_Fca126_mat1.0_genomic.fna.gz GCF_018350175.1_F.catus_Fca126_mat1.0_genomic.gff.gz exome_fcatus_fca126_mat1_k51_s10k.fa

snipe sketch --amplicon exome_fcatus_fca126_mat1_k51_s10k.fa -c 8 -n exome_fcatus_fca126_mat1_k51_s10k -o exome_fcatus_fca126_mat1_k51_s10k.zip

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All sigs were uploaded to OSF.

Analysis

wget --content-disposition https://osf.io/ap8xk/download
wget --content-disposition https://osf.io/ar2cg/download
wget --content-disposition https://osf.io/tbcu8/download
wget --content-disposition https://osf.io/7fgj5/download

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Merge runs to exps