Commit 583f249e authored by Safia Saci's avatar Safia Saci
Browse files

Update annotationBlocksCount_sarray.sh

parent 18a54f27
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fasted_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fasted_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fasted_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fasted_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R5.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fasted_R5.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R6.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fasted_R6.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fed_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fed_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fed_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fed_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R5.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11-_fed_R5.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fasted_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fasted_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fasted_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fasted_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R5.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fasted_R5.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R6.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fasted_R6.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fed_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fed_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fed_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fed_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R5.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fed_R5.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R6.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o G11+_fed_R6.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-input_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o Tem-input_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-input_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o Tem-input_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-input_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o Tem-input_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-input_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o Tem-input_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-methyl_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o Tem-methyl_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-methyl_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o Tem-methyl_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-methyl_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o Tem-methyl_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-methyl_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_genome.RDS -o Tem-methyl_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fasted_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fasted_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fasted_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fasted_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R5.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fasted_R5.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fasted_R6.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fasted_R6.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fed_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fed_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fed_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fed_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11-_fed_R5.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11-_fed_R5.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fasted_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fasted_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fasted_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fasted_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R5.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fasted_R5.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fasted_R6.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fasted_R6.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fed_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fed_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fed_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fed_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R5.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fed_R5.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/G11+_fed_R6.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o G11+_fed_R6.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-input_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o Tem-input_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-input_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o Tem-input_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-input_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o Tem-input_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-input_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o Tem-input_R4.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-methyl_R1.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o Tem-methyl_R1.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-methyl_R2.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o Tem-methyl_R2.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-methyl_R3.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o Tem-methyl_R3.rds
./annotationBlocksCount.R -i /work2/genphyse/genepi/data/porc/medpseq/ROSEpigs_processed2/results/bwa/mergedLibrary/Tem-methyl_R4.mLb.clN.sorted.bam -w /work2/genphyse/genepi/guillaume/rosepigs/windows_full_genome.RDS -o Tem-methyl_R4.rds
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