renku run ./code/merge.sh ./data/mapped/CCO1.HTseq ./data/mapped/CCO2.HTseq ./data/mapped/CCO3.HTseq ./data/mapped/EV1.HTseq ./data/mapped/EV2.HTseq ./data/mapped/EV3.HTseq ./data/mapped/HIS1.HTseq ./data/mapped/HIS2.HTseq ./data/mapped/HIS3.HTseq

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/HIS3Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/HIS2Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/HIS1Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/EV3Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/EV2Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/EV1Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/CCO3Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/CCO2Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run htseq-count -f bam -r pos -s reverse -m union -t exon -i gene_id ./data/mapped/CCO1Aligned.sortedByCoord.out.bam ./data/wbcel235/celegans-genome/Caenorhabditis_elegans.WBcel235.89.gtf.gz

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/HIS3_L1_R1_001_iJ5odUOz5hnK.fastq.gz ./data/fastq/HIS3_L1_R1_002_oWBEHe65ouLY.fastq.gz ./data/fastq/HIS3_L1_R1_003_xfbNyg2J0vyg.fastq.gz --outFileNamePrefix ./data/mapped/HIS3

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/HIS2_L1_R1_001_mBAlZjLFy4ti.fastq.gz ./data/fastq/HIS2_L1_R1_002_VhYBgEw6UOXL.fastq.gz ./data/fastq/HIS2_L1_R1_003_pCkDrgHLXRKh.fastq.gz --outFileNamePrefix ./data/mapped/HIS2

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/HIS1_L1_R1_001_k9f7bBQ83TFv.fastq.gz ./data/fastq/HIS1_L1_R1_002_IoIvJJ4HpgVO.fastq.gz ./data/fastq/HIS1_L1_R1_003_eNryFIADR6C0.fastq.gz --outFileNamePrefix ./data/mapped/HIS1

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/EV3_L1_R1_001_GadUC4NHCqeW.fastq.gz ./data/fastq/EV3_L1_R1_002_pI9ZffqmNbZV.fastq.gz ./data/fastq/EV3_L1_R1_003_FuTJ4Iwc3QvM.fastq.gz ./data/fastq/EV3_L1_R1_004_V2cDUfQqjLVM.fastq.gz --outFileNamePrefix ./data/mapped/EV3

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/EV2_L1_R1_001_AdoWBYAz9Ef8.fastq.gz ./data/fastq/EV2_L1_R1_002_cX9dFjFShIaf.fastq.gz ./data/fastq/EV2_L1_R1_003_JG0e2mI1vg0V.fastq.gz --outFileNamePrefix ./data/mapped/EV2

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/EV1_L1_R1_001_K1lVAcPpBPGP.fastq.gz ./data/fastq/EV1_L1_R1_002_qOUCQZPWOXR3.fastq.gz ./data/fastq/EV1_L1_R1_003_WQ2w0S6IZq9J.fastq.gz --outFileNamePrefix ./data/mapped/EV1

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/CCO3_L1_R1_001_4FUJJpxSolRO.fastq.gz ./data/fastq/CCO3_L1_R1_002_SCWplqJdeilE.fastq.gz ./data/fastq/CCO3_L1_R1_003_oUHoSAID4wz1.fastq.gz --outFileNamePrefix ./data/mapped/CCO3

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/CCO2_L1_R1_001_4XbZOyHUhHGi.fastq.gz ./data/fastq/CCO2_L1_R1_002_oQtPwZmwoob8.fastq.gz ./data/fastq/CCO2_L1_R1_003_kdzoXvrCF5uU.fastq.gz --outFileNamePrefix ./data/mapped/CCO2

renku run ./code/cmd.sh --runThreadN 14 --genomeDir ./data/genome/celegans-genome/ --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --readFilesIn ./data/fastq/CCO1_L1_R1_001_NVyMwfiCHYbh.fastq.gz ./data/fastq/CCO1_L1_R1_002_6NXgFqelHo0F.fastq.gz ./data/fastq/CCO1_L1_R1_003_C6yjwgTZU6Sy.fastq.gz --outFileNamePrefix ./data/mapped/CCO1

renku dataset add --relative-to /Users/bouillet/git/renku-maroun/fastq fastq /Users/bouillet/git/renku-maroun/fastq

renku dataset add wbcel235 --relative-to data/celegans -t data/celegans https://renkulab.io/gitlab/erbou/celegans-genome.git

renku dataset add genome --relative-to genome -t genome https://renkulab.io/gitlab/erbou/celegans-genome.git