Commit c052f458 authored by Holger Brandl's avatar Holger Brandl

fixed mouse igenome build

parent a320236a
......@@ -38,10 +38,12 @@ openFasta(File(args[0])).
filterNot { it.description!!.contains("dna:scaffold") }.
forEach { print(it.toEntryString()) }
EOF
grep -F ">" genome.fa
samtools faidx genome.fa &
mcdir ${IGENOME_BASE}/Annotation
mcdir ${IGENOME_BASE}/Annotation/Genes
wget ftp://ftp.ensembl.org/pub/release-88/gtf/homo_sapiens/Homo_sapiens.GRCh38.88.gtf.gz
......@@ -58,13 +60,13 @@ jl submit "~/bin/bowtie-1.1.2/bowtie-build ${IGENOME_BASE}/Sequence/WholeGenomeF
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"
jl submit -w 5:00 -m 50g "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
mkdir ${IGENOME_BASE}/Sequence/KallistoIndex
wget ftp://ftp.ensembl.org/pub/release-92/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.cdna.all.fa.gz
refFasta=cdna.fasta
refFasta=${IGENOME_BASE}/Sequence/KallistoIndex/cdna.fasta
gunzip -c *.cdna.all.fa.gz > ${refFasta}
jl submit "kallisto index -i ${refFasta}.kallisto.idx ${refFasta}"
......
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