Commit defed22f authored by Lena Hersemann's avatar Lena Hersemann
Browse files

added igenome for Mus musculus Ensembl v103 and GRCm39

parent a2f5f62d
screen -R igenome_build
export NGS_TOOLS="/projects/bioinfo/$(whoami)/scripts/ngs_tools"
umask u=rwx,g=rwx,o=
ls "${NGS_TOOLS}" >/dev/null || { echo "not all project resources are well defined" 1>&2; exit 1; }
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
export PATH=${NGS_TOOLS}/dge_workflow:$PATH
#-----------------------------------------------------------------------------------------------------------------------
## set up genome assembly
IGENOME_BASE=/projects/bioinfo/igenomes/Mus_musculus/Ensembl_v103/GRCm39
mcdir ${IGENOME_BASE}
mcdir ${IGENOME_BASE}/Sequence/WholeGenomeFasta
wget ftp://ftp.ensembl.org/pub/release-103/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz
gunzip -c Mus_musculus.GRCm39.dna.primary_assembly.fa.gz > genome.fa
grep -F ">" genome.fa
samtools faidx genome.fa &
## set up genome annotation
mcdir ${IGENOME_BASE}/Annotation/Genes
wget ftp://ftp.ensembl.org/pub/release-103/gtf/mus_musculus/Mus_musculus.GRCm39.103.gtf.gz
gunzip -c Mus_musculus.GRCm39.103.gtf.gz > genes.gtf
#head genes.gtf
ll ${IGENOME_BASE}/Sequence/WholeGenomeFasta/genome.fa
dge_create_star_index ${IGENOME_BASE} &
mkdir ${IGENOME_BASE}/Sequence/BowtieIndex
jl submit "bowtie-build ${IGENOME_BASE}/Sequence/WholeGenomeFasta/genome.fa ${IGENOME_BASE}/Sequence/BowtieIndex/genome"
ln -s ${IGENOME_BASE}/Sequence/WholeGenomeFasta/genome.fa ${IGENOME_BASE}/Sequence/BowtieIndex/genome.fa
mkdir ${IGENOME_BASE}/Sequence/Bowtie2Index
jl submit "bowtie2-build ${IGENOME_BASE}/Sequence/WholeGenomeFasta/genome.fa ${IGENOME_BASE}/Sequence/Bowtie2Index/genome"
ln -s ${IGENOME_BASE}/Sequence/WholeGenomeFasta/genome.fa ${IGENOME_BASE}/Sequence/Bowtie2Index/genome.fa
mcdir ${IGENOME_BASE}/Sequence/KallistoIndex
wget ftp://ftp.ensembl.org/pub/release-103/fasta/mus_musculus/cdna/Mus_musculus.GRCm39.cdna.all.fa.gz
refFasta=cdna.fasta
gunzip -c *.cdna.all.fa.gz > ${refFasta}
jl submit "kallisto index -i ${refFasta}.kallisto.idx ${refFasta}"
cd /projects/bioinfo/igenomes/Mus_musculus
chmod -R ugo-w Ensembl_v103
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