Commit 05ee5f64 authored by Lena Hersemann's avatar Lena Hersemann

added new human igenome build (Ensembl release 94)

parent 789f0572
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/Homo_sapiens/Ensembl_v95_custom/GRCh38_p12
#IGENOME_BASE=/net/mack/lustre/projects/bioinfo/igenomes/Homo_sapiens/Ensembl_v95_custom/GRCh38_p12
mcdir ${IGENOME_BASE}
mcdir ${IGENOME_BASE}/Sequence/WholeGenomeFasta
wget ftp://ftp.ensembl.org/pub/release-95/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz
gunzip -c Homo_sapiens.GRCh38.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-95/gtf/homo_sapiens/Homo_sapiens.GRCh38.95.gtf.gz
gunzip -c Homo_sapiens.GRCh38.95.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-95/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz
refFasta=cdna.fasta
gunzip -c *.cdna.all.fa.gz > ${refFasta}
jl submit "kallisto index -i ${refFasta}.kallisto.idx ${refFasta}"
chmod -R a-w /projects/bioinfo/igenomes/Homo_sapiens/Ensembl_v95_custom
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