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test: transcript gene more
transcript:
${TRINITY_HOME}/util/misc/contig_ExN50_statistic.pl ../test_DATA/salmon-quasi-trans.isoform.TMM.EXPR.matrix ../test_DATA/Trinity.fasta transcript > test.transcript.ExN50
${TRINITY_HOME}/util/misc/plot_ExN50_statistic.Rscript test.transcript.ExN50
${TRINITY_HOME}/util/misc/try_estimate_TPM_filtering_threshold.Rscript --E_inputs salmon-quasi-trans.isoform.TMM.EXPR.matrix.by-transcript.E-inputs --out_pdf estimate_TPM_threshold.by_gene.pdf
gene:
${TRINITY_HOME}/util/misc/contig_ExN50_statistic.pl ../test_DATA/salmon-quasi-trans.isoform.TMM.EXPR.matrix ../test_DATA/Trinity.fasta gene > test.gene.ExN50
${TRINITY_HOME}/util/misc/plot_ExN50_statistic.Rscript test.gene.ExN50
${TRINITY_HOME}/util/misc/try_estimate_TPM_filtering_threshold.Rscript --E_inputs salmon-quasi-trans.isoform.TMM.EXPR.matrix.by-gene.E-inputs --out_pdf estimate_TPM_threshold.by_gene.pdf
more: acanth mouse axolotl
acanth:
${TRINITY_HOME}/util/misc/plot_ExN50_statistic.Rscript more_examples/acanth.ExN50.stats
${TRINITY_HOME}/util/misc/try_estimate_TPM_filtering_threshold.Rscript --E_inputs more_examples/acanth.E-inputs.gz --out_pdf acanth.threshold_estimate.pdf
mouse:
${TRINITY_HOME}/util/misc/plot_ExN50_statistic.Rscript more_examples/mouse.50M.ExN50.stats
${TRINITY_HOME}/util/misc/try_estimate_TPM_filtering_threshold.Rscript --E_inputs more_examples/mouse50M.E-inputs.gz --out_pdf mouse50M.threshold_estimate.pdf
axolotl:
${TRINITY_HOME}/util/misc/plot_ExN50_statistic.Rscript more_examples/axolotl.transcript.ExN50.stats
${TRINITY_HOME}/util/misc/plot_ExN50_statistic.Rscript more_examples/axolotl.gene.ExN50.stats
clean:
rm -f ./salmon* ./test.* ./estimate_TPM_threshold* ./*.pdf
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