Commit f95fa905 authored by domingue's avatar domingue

Converted gff3 to gtf which was causing STAR to crash - needs a gtf

parent 657cb4bc
......@@ -149,8 +149,75 @@ jl wait --email
wait # for samtools and star-index creation
## Schmidtea mediterranea
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/Schmidtea_mediterranea/PlanMinev3.0/S2F2
mkdir -p ${IGENOME_BASE}
mkdir -p ${IGENOME_BASE}/Sequence/WholeGenomeFasta
cd ${IGENOME_BASE}/Sequence/WholeGenomeFasta
wget http://planmine.mpi-cbg.de/planmine/model/bulkdata/dd_Smes_g4.fasta.zip
# zcat dd_Smes_g4.fasta.zip | grep "^>"
zcat dd_Smes_g4.fasta.zip > genome.fa &&
rm dd_Smes_g4.fasta.zip
samtools faidx genome.fa &
mkdir -p ${IGENOME_BASE}/Annotation/Genes
cd ${IGENOME_BASE}/Annotation/Genes
wget http://planmine.mpi-cbg.de/planmine/model/bulkdata/smes_v2_repeatfilt_SMESG.gff3.zip
gunzip -c smes_v2_repeatfilt_SMESG.gff3.zip > genes.gff3
# head -n 500 genes.gtf
# convert gene annotation to GTF due to issues with STAR. See https://groups.google.com/forum/#!topic/rna-star/PgmFHeHoquQ
append2path ${BIO_BIN_BASE}/gffread-0.11.4
gffread -T genes.gff3 -o genes.gtf
ll ${IGENOME_BASE}/Sequence/WholeGenomeFasta/genome.fa
dge_create_star_index ${IGENOME_BASE} &
mcdir ${IGENOME_BASE}/Sequence
mkdir ${IGENOME_BASE}/Sequence/BowtieIndex
jl submit -w 10:00 -m 50g "/projects/bioinfo/brandl/bin/bowtie-1.2.1.1/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 -w 10:00 -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
mcdir ${IGENOME_BASE}/Sequence/KallistoIndex
wget http://planmine.mpi-cbg.de/planmine/model/bulkdata/SMEST.1.pcf.contigs.fasta.zip
refFasta=cdna.fasta
gunzip -c SMEST.1.pcf.contigs.fasta.zip > ${refFasta}
jl submit --wait "kallisto index -i ${refFasta}.kallisto.idx ${refFasta}" &
jl wait --email
wait # for samtools and star-index creation
########################################################################################################################
## sync igenomes between bioninfo and cluster
## sync igenomes between bioinfo and cluster
# tag as rw
......
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