Commit 2c7e0c8c authored by domingue's avatar domingue

Added marmoset genome

parent 7d5cb986
......@@ -215,6 +215,43 @@ jl wait --email
wait # for samtools and star-index creation
## Marmoset, Callithrix jacchus
cd /projects/bioinfo/igenomes
export NGS_TOOLS="/projects/bioinfo/$(whoami)/scripts/ngs_tools"
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
source <(curl https://git.mpi-cbg.de/bioinfo/datautils/raw/v1.42/bash/core_utils.sh 2>&1 2>/dev/null)
umask u=rwx,g=rwx,o=
ls "${NGS_TOOLS}" >/dev/null || { echo "not all project resources are well defined" 1>&2; exit 1; }
export PATH=${NGS_TOOLS}/dge_workflow:$PATH
IGENOME_BASE=/projects/bioinfo/igenomes/Callithrix_jacchus/Ensembl_v97/ASM275486v1
mkdir -p ${IGENOME_BASE}
mkdir -p ${IGENOME_BASE}/Sequence/WholeGenomeFasta
cd ${IGENOME_BASE}/Sequence/WholeGenomeFasta
wget ftp://ftp.ensembl.org/pub/release-97/fasta/callithrix_jacchus/dna/Callithrix_jacchus.ASM275486v1.dna.toplevel.fa.gz
zcat Callithrix_jacchus.ASM275486v1.dna.toplevel.fa.gz > genome.fa &&
rm Callithrix_jacchus.ASM275486v1.dna.toplevel.fa.gz
samtools faidx genome.fa &
mkdir -p ${IGENOME_BASE}/Annotation/Genes
cd ${IGENOME_BASE}/Annotation/Genes
wget ftp://ftp.ensembl.org/pub/release-97/gtf/callithrix_jacchus/Callithrix_jacchus.ASM275486v1.97.gtf.gz
zcat Callithrix_jacchus.ASM275486v1.97.gtf.gz > genes.gtf &
rm Callithrix_jacchus.ASM275486v1.97.gtf.gz
########################################################################################################################
## sync igenomes between bioinfo and cluster
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment