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test: test_edgeR test_DESeq2 test_voom test_ROTS test_PtR_PCA
test_edgeR:
../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method edgeR -s samples.txt -o edgeR_outdir
cd edgeR_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
test_DESeq2:
ifeq "" "$(shell which DESeq2)"
echo skipping DESeq2 test
else
../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method DESeq2 -s samples.txt -o DESeq2_outdir
cd DESeq2_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
endif
test_voom:
../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method voom -s samples.txt -o voom_outdir
cd voom_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
test_ROTS:
# disabled for now
#../../Analysis/DifferentialExpression/run_DE_analysis.pl -m Trinity_trans.counts.matrix --method ROTS -s samples.txt -o ROTS_outdir --ROTS_B 50 # make it go faster, use more in practice
#cd ROTS_outdir && ../../../Analysis/DifferentialExpression/analyze_diff_expr.pl --matrix ../Trinity_trans.TMM.EXPR.matrix --samples ../samples.txt
test_PtR_PCA:
../../Analysis/DifferentialExpression/PtR -m Trinity_trans.TMM.EXPR.matrix -s samples.txt --prin_comp 3 --add_prin_comp_heatmaps 30
clean:
rm -rf ./edgeR_outdir
rm -rf ./DESeq2_outdir
rm -rf ./voom_outdir
rm -rf ./ROTS_outdir
rm -f ./Trinity_trans.counts.matrix.*
rm -f ./Trinity_trans.TMM.EXPR.matrix.*
rm -f ./*.pdf
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