Commit c320c318 authored by Holger Brandl's avatar Holger Brandl
Browse files

added mm9 igenome setup

parent c2e112ea
......@@ -171,3 +171,19 @@ wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.2-1/sratoolkit.2.8.2-1-ubuntu
tar xvf sratoolkit.2.8.2-1-ubuntu64.tar.gz
#cd sratoolkit.2.8.2-1-ubuntu64/bin
#./fastq-dump -h
########################################################################################################################
## iGenomes
cd /local2/igenomes
mcdir temp
wget ftp://igenome:G3nom3s4u@ussd-ftp.illumina.com/Mus_musculus/Ensembl/NCBIM37/Mus_musculus_Ensembl_NCBIM37.tar.gz
tar xvf Mus_musculus_Ensembl_NCBIM37.tar.gz
## here: extract annoation version and rename sub-folder accordingly
## build star index
export NGS_TOOLS=/net/mack/lustre/projects/bioinfo/scripts/ngs_tools/dev
source ${NGS_TOOLS}/dge_workflow/dge_utils.sh
dge_create_star_index /local2/igenomes/Mus_Musculus/Ensembl/NCBIM37__ens66_july2015
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