run107 Barcode Name Sample Bases >=Q20 Bases Reads Mean Read Length IonXpressRNA_010 SCR14 1675181557 1492520215 14801845 113 bp DrSCereghini_4RNAseqsamples_SCR13-E145-3wt-bc2_SCR14-E145-5Het-bc10_SCR14 has been repurified 141104 Barcode Name Sample Bases >=Q20 Bases Reads Mean Read Length run118 IonXpressRNA_016 SCR15 4579823958 3683884586 38631875 118 bp ITlab_MS4ChIP_ITC42-InF13-BC3_ITC43-InKO1-BC10_ITC38-HF13-BC2_DrSCereghini_4RNAseq_SCR15-E145HET7-bc16 ./cuffquant-hg19.sh &>cuffquant-hg19.log & (wd: /data/images/proton/run90/pairings) @@ get WT sig DE awk '{if ($NF=="yes"){print $0}}' 0h_VS_1h_wt/cuffdiff2_GM-tr-0h-a_vs_GM-tr-1h-a/gene_exp.diff >> wt-significant2.txt awk '{if ($NF=="yes"){print $0}}' 0h_VS_3h_wt/cuffdiff2_GM-tr-0h-a_vs_GM-tr-3h-a/gene_exp.diff >> wt-significant2.txt awk '{if ($NF=="yes"){print $0}}' untr0h_VS_tr0h_wt/cuffdiff2_GM-tr-0h-a_vs_GM-untr-0h-a/gene_exp.diff >> wt-significant2.txt awk '{if ($NF=="yes"){print $0}}' untr_VS_tr_wt/cuffdiff2_GM-tr-0h-a_vs_GM-untr-0h-a/gene_exp.diff >> wt-significant2.txt awk '{o[$1]=$0}END{for (i in o) print o[i]}' wt-significant2.txt > wt-significant2-uniq.txt wc wt-significant2* 182 2548 21730 wt-significant2.txt 171 2394 20380 wt-significant2-uniq.txt awk -v f="../wt-significant2-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.attr_table > genes.attr_table-wt2.csv awk -v f="../wt-significant2-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.fpkm_table > genes.fpkm_table-wt2.csv awk -v f="../wt-significant2-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.count_table > genes.count_table-wt2.csv join --header genes.fpkm_table-wt2.csv genes.attr_table-wt2.csv > genes.fpkm_attr_table-wt2.csv awk '{if ($NF=="yes"){print $0}}' 0h_VS_1h_wt/cuffdiff_GM-tr-0h-a_vs_GM-tr-1h-a/gene_exp.diff >> wt-significant.txt awk '{if ($NF=="yes"){print $0}}' 0h_VS_3h_wt/cuffdiff_GM-tr-0h-a_vs_GM-tr-3h-a/gene_exp.diff >> wt-significant.txt awk '{if ($NF=="yes"){print $0}}' untr0h_VS_tr0h_wt/cuffdiff_GM-tr-0h-a_vs_GM-untr-0h-a/gene_exp.diff >> wt-significant.txt awk '{if ($NF=="yes"){print $0}}' untr_VS_tr_wt/cuffdiff_GM-tr-0h-a_vs_GM-untr-0h-a/gene_exp.diff >> wt-significant.txt awk '{o[$1]=$0}END{for (i in o) print o[i]}' wt-significant.txt > wt-significant-uniq.txt 182 2548 21730 wt-significant.txt 171 2394 20380 wt-significant-uniq.txt awk -v f="../wt-significant-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.attr_table > genes.attr_table-wt.csv awk -v f="../wt-significant-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.fpkm_table > genes.fpkm_table-wt.csv awk -v f="../wt-significant-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.count_table > genes.count_table-wt.csv join --header genes.fpkm_table-wt.csv genes.attr_table-wt.csv > genes.fpkm_attr_table-wt.csv awk '{if ($NF=="yes"){print $0}}' 1h_wt_VS_1h_scan/cuffdiff_GM-tr-1h-a_vs_SCAN-tr-1h-a/gene_exp.diff >> scan-significant.txt awk '{if ($NF=="yes"){print $0}}' 3h_wt_VS_3h_scan/cuffdiff_GM-tr-3h-a_vs_SCAN-tr-3h-a/gene_exp.diff >> scan-significant.txt awk '{o[$1]=$0}END{for (i in o) print o[i]}' scan-significant.txt > scan-significant-uniq.txt 2816 39424 357028 scan-significant.txt 2105 29470 264338 scan-significant-uniq.txt awk -v f="../scan-significant-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.attr_table > genes.attr_table-scan.csv awk -v f="../scan-significant-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.fpkm_table > genes.fpkm_table-scan.csv awk -v f="../scan-significant-uniq.txt" -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.count_table > genes.count_table-scan.csv join --header genes.fpkm_table-scan.csv genes.attr_table-scan.csv > genes.fpkm_attr_table-scan.csv @@get all sig DE genes reczko@n2:/data/results/reference/Ccap/tr2/run111$ for i in */cuffdiff_*/gene_exp.diff do awk '{if ($NF=="yes"){print $0}}' $i >> all-significant.txt done awk '{o[$1]=$0}END{for (i in o) print o[i]}' all-significant.txt > all-significant-uniq.txt wc all-* 5087 71218 656181 all-significant.txt 3353 46942 430281 all-significant-uniq.txt awk -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.attr_table > genes.attr_table.csv awk -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.fpkm_table > genes.fpkm_table.csv awk -f /data/results/tools/rnaseq/cuffnorm-filter-xlocs1.awk genes.count_table > genes.count_table.csv join --header genes.fpkm_table.csv genes.attr_table.csv > genes.fpkm_attr_table.csv #next steps descr. in: /data/images/proton/run90/pairings/cuffnorm/README-heatmaps.txt @@ /data/results/tools/rnaseq/metaseqr/test_run84/process_run107.txt zcat /data/results/tools/rnaseq/metaseqr/test_run84/metaseqr_wt_vs_het_mm9_test2/lists/normalized_counts_table.txt.gz | head chromosome start end gene_id gc_content strand gene_name biotype wtSCR13-E145-3 wtSCR10-E145-4 hetSCR15-E145-7 hetSCR12-E145-6 chr1 4481008 4487435 NM_011441 0.4975 - Sox17 protein_coding 443 665 752 695 chr1 4763278 4775807 NM_001177658 0.4259 - Mrpl15 protein_coding 1814 1146 1561 1669