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#!/bin/bash
set -ex
aligner=$1
if [ -z ${aligner} ]; then
echo
echo "usage: $0 STAR|HISAT2"
echo
exit 1
fi
${TRINITY_HOME}/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl --genes_fasta minigenome.fa --genes_gtf minigenome.gtf --samples_file samples.txt --out_prefix ${aligner}-G --aligner ${aligner}
${TRINITY_HOME}/Analysis/SuperTranscripts/Trinity_gene_splice_modeler.py --trinity_fasta mini.Trinity_fmt.fasta --out_prefix trinSuper --no_squeeze --no_refinement
${TRINITY_HOME}/Analysis/SuperTranscripts/DTU/dexseq_wrapper.pl --genes_fasta trinSuper.fasta --genes_gtf trinSuper.gtf --samples_file samples.txt --out_prefix ${aligner}-S --aligner ${aligner}
./compare_dexseq_results.pl ${aligner}-G.dexseq.results.dat ${aligner}-S.dexseq.results.dat > ${aligner}-compare.dat
cat ${aligner}-compare.dat | perl -lane '@x = split(/\t/); push (@x, abs(log($x[1]+1e-50) - log($x[3]+1e-50))); print join("\t", @x);' | sort -k 6,6g > ${aligner}-compare.dat.delta
./plot_comparison.Rscript ${aligner}-compare.dat
# require at least min 0.95 correlation between genome and supertranscript based analysis
./test_for_cor.sh ${aligner}-compare.dat.cor 0.9
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