prepare_qtl_metadata.lsf

#BSUB -J prepare_qtl_metadata
#BSUB -P acc_als-omics
#BSUB -q express
#BSUB -n 1
#BSUB -R span[ptile=1]
#BSUB -R rusage[mem=50000]
#BSUB -W 06:00
#BSUB -o %J.stdout
#BSUB -eo %J.stderr
#BSUB -L /bin/bash

#GTF="/sc/arion/projects/als-omics/microglia_isoseq/Erica/references/combined_063022.gtf"
#CODE="gencode_v38_isoseq_novel_tx"
JUNCTIONS="leafcutter/all_junctions_v2.txt"

GTF="/sc/arion/projects/ad-omics/data/references/hg38_reference/GENCODE/gencode.v38.primary_assembly/gencode.v38.primary_assembly.annotation.gtf"
CODE="gencode_v38"

GTF="/sc/arion/projects/als-omics/microglia_isoseq/isoseq-pipeline/results/stringtie2/combine/raj_roussos_0922_stringtie_mix_combined.sorted.gtf.gz"
CODE="gencode_novel"

# make SUPPA events
export PS1=""; ml anaconda3; CONDA_BASE=$(conda info --base); source $CONDA_BASE/etc/profile.d/conda.sh
module purge
conda activate isoseq-pipeline
ml R/4.0.3

main () { # SKIP THIS FOR NOW

mkdir -p SUPPA/${CODE}/
suppa.py generateEvents -i $GTF -o SUPPA/${CODE}/${CODE} -e SE SS MX RI FL -f ioe
}

mkdir -p input
# make gene annotation
Rscript scripts/get_gene_meta_from_gtf.R  --gtf $GTF --mode gene --prefix input/${CODE}
# make exon annotation
Rscript scripts/get_gene_meta_from_gtf.R  --gtf $GTF --mode exon --prefix input/${CODE}
# make transcript annotation
Rscript scripts/get_gene_meta_from_gtf.R  --gtf $GTF --mode transcript  --prefix input/${CODE}

main () {
# REMOVE LATER
# make leafcutter matrix - slow
mkdir -p leafcutter
Rscript scripts/prepare_leafcutter_matrix.R --prefix leafcutter/${CODE}  --junctions $JUNCTIONS --exons input/${CODE}_exon_pheno_meta.tsv  
}