Commit b64e5c47 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Update for isoforms.

parent 96b61dc3
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......@@ -14,27 +14,27 @@
module load iGenomes/2013-03-25
module load RSEM/1.2.31
rsem-generate-data-matrix /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALK_RIP1_PI/gene-counts.sh-1.0.0/ALK_RIP1_PI_AGTCAA_L006_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALK_RIP2_PI/gene-counts.sh-1.0.0/ALK_RIP2_PI_GTTTCG_L007_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALK_RIP1_PARP1/gene-counts.sh-1.0.0/ALK_RIP1_PARP1_AGTTCC_L006_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALK_RIP2_PARP1/gene-counts.sh-1.0.0/ALK_RIP2_PARP1_CGTACG_L006_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
rsem-generate-data-matrix /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALK_RIP1_PI/gene-counts.sh-1.0.0/ALK_RIP1_PI_AGTCAA_L006_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALK_RIP2_PI/gene-counts.sh-1.0.0/ALK_RIP2_PI_GTTTCG_L007_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALK_RIP1_PARP1/gene-counts.sh-1.0.0/ALK_RIP1_PARP1_AGTTCC_L006_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALK_RIP2_PARP1/gene-counts.sh-1.0.0/ALK_RIP2_PARP1_CGTACG_L006_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
> /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/gene_matrix/ALK.txt
rsem-generate-data-matrix /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALKT_RIP1_PI/gene-counts.sh-1.0.0/ALKT_RIP1_PI_ATGTCA_L003_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALKT_RIP2_PI/gene-counts.sh-1.0.0/ALKT_RIP2_PI_GAGTGG_L003_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALKT_RIP1_PARP1/gene-counts.sh-1.0.0/ALKT_RIP1_PARP1_CCGTCC_L006_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALKT_RIP2_PARP1/gene-counts.sh-1.0.0/ALKT_RIP2_PARP1_GGTAGC_L006_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
rsem-generate-data-matrix /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALKT_RIP1_PI/gene-counts.sh-1.0.0/ALKT_RIP1_PI_ATGTCA_L003_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALKT_RIP2_PI/gene-counts.sh-1.0.0/ALKT_RIP2_PI_GAGTGG_L003_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALKT_RIP1_PARP1/gene-counts.sh-1.0.0/ALKT_RIP1_PARP1_CCGTCC_L006_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_ALKT_RIP2_PARP1/gene-counts.sh-1.0.0/ALKT_RIP2_PARP1_GGTAGC_L006_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
> /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/gene_matrix/ALKT.txt
rsem-generate-data-matrix /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLK_RIP1_PI/gene-counts.sh-1.0.0/MLK_RIP1_PI_ACAGTG_L006_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLK_RIP2_PI/gene-counts.sh-1.0.0/MLK_RIP2_PI_GTTTCG_L008_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLK_RIP1_PARP1/gene-counts.sh-1.0.0/MLK_RIP1_PARP1_GCCAAT_L005_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLK_RIP2_PARP1/gene-counts.sh-1.0.0/MLK_RIP2_PARP1_CGTACG_L005_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
rsem-generate-data-matrix /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLK_RIP1_PI/gene-counts.sh-1.0.0/MLK_RIP1_PI_ACAGTG_L006_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLK_RIP2_PI/gene-counts.sh-1.0.0/MLK_RIP2_PI_GTTTCG_L008_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLK_RIP1_PARP1/gene-counts.sh-1.0.0/MLK_RIP1_PARP1_GCCAAT_L005_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLK_RIP2_PARP1/gene-counts.sh-1.0.0/MLK_RIP2_PARP1_CGTACG_L005_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
> /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/gene_matrix/MLK.txt
rsem-generate-data-matrix /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP1_PI/gene-counts.sh-1.0.0/MLKE_RIP1_PI_CAGATC_L006_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP2_PI/gene-counts.sh-1.0.0/MLKE_RIP2_PI_GAGTGG_L008_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP1_PARP1_SecondRun/gene-counts.sh-1.0.0/MLKE_RIP1_PARP1_ACTTGA_L004_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP2_PARP1_16/gene-counts.sh-1.0.0/MLKE_RIP2_PARP1_16_CCGTCC_L007_R1.rDNA.filtered.fastq.gz_filtered.genes.results \
rsem-generate-data-matrix /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP1_PI/gene-counts.sh-1.0.0/MLKE_RIP1_PI_CAGATC_L006_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP2_PI/gene-counts.sh-1.0.0/MLKE_RIP2_PI_GAGTGG_L008_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP1_PARP1_SecondRun/gene-counts.sh-1.0.0/MLKE_RIP1_PARP1_ACTTGA_L004_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
/project/GCRB/Lee_Lab/s163035/DK_RIP-seq/PARP1_RIPseq_in_AC16_MCF7_withTNFa_E2/raw/Sample_MLKE_RIP2_PARP1_16/gene-counts.sh-1.0.0/MLKE_RIP2_PARP1_16_CCGTCC_L007_R1.rDNA.filtered.fastq.gz_filtered.isoforms.results \
> /project/GCRB/Lee_Lab/s163035/DK_RIP-seq/gene_matrix/MLKE.txt
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