Template_to_generate_figures.sh

python /scr1/users/xuy2/TEQUILA_GEO_data/GitHub_test/scripts/scripts/2_2_Generate_bar_structure_figure_example.py --gene ENSG00000141510 --gene_name TP53 --transcript ESPRESSO:chr17:1864:802 --abundance_CPM_original BRCA_Example/samples_N2_R0_abundance_CPM_ESPRESSO.txt --abundance_proportion BRCA_Example/samples_N2_R0_abundance_CPM_ESPRESSO_proportion_reshaped_merge_others.txt --abundance_CPM BRCA_Example/samples_N2_R0_abundance_CPM_ESPRESSO_reshaped_merge_others.txt --bedgraph BRCA_Example/samples_BedGraph.bed --sorted_group Basal_B,Basal_A,HER2_Amp,Luminal --out_dir BRCA_Example/Example_res --figures Isoform Single_isoform Structure --canonical_transcript /scr1/users/xuy2/TEQUILA_GEO_data/GitHub_test/scripts/scripts/files/Gencode_v39_canonical_isoform.txt --basic_transcript /scr1/users/xuy2/TEQUILA_GEO_data/GitHub_test/scripts/scripts/files/gencode.v34lift37.annotation_basic_trans.txt --anno_gtf /scr1/users/xuy2/TEQUILA_GEO_data/GitHub_test/scripts/scripts/files/gencode.v34lift37.annotation.gtf --genome_version hg19 --order yes

python /scr1/users/xuy2/TEQUILA_GEO_data/GitHub_test/scripts/scripts/2_2_Generate_bar_structure_figure_example.py --gene ENSG00000088305 --gene_name DNMT3B --transcript ENST00000348286 --abundance_CPM_original BRCA_Example/samples_N2_R0_abundance_CPM_ESPRESSO.txt --abundance_proportion BRCA_Example/samples_N2_R0_abundance_CPM_ESPRESSO_proportion_reshaped_merge_others.txt --abundance_CPM BRCA_Example/samples_N2_R0_abundance_CPM_ESPRESSO_reshaped_merge_others.txt --bedgraph BRCA_Example/samples_BedGraph.bed --sorted_group Basal_B,Basal_A,HER2_Amp,Luminal --out_dir BRCA_Example/Example_res --figures Isoform Single_isoform Structure --canonical_transcript /scr1/users/xuy2/TEQUILA_GEO_data/GitHub_test/scripts/scripts/files/Gencode_v39_canonical_isoform.txt --basic_transcript /scr1/users/xuy2/TEQUILA_GEO_data/GitHub_test/scripts/scripts/files/gencode.v34lift37.annotation_basic_trans.txt --anno_gtf /scr1/users/xuy2/TEQUILA_GEO_data/GitHub_test/scripts/scripts/files/gencode.v34lift37.annotation.gtf --genome_version hg19 --order yes