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- samtools sort F11_S11_L001_R1_001.fastq.gz.subread.BAM > F11.sorted.bam; samtools sort F1_S1_L001_R1_001.fastq.gz.subread.BAM > F1.sorted.bam ; samtools sort F2_S2_L001_R1_001.fastq.gz.subread.BAM > F2.sorted.bam ;samtools sort F3_S3_L001_R1_001.fastq.gz.subread.BAM > F3.sorted.bam ; samtools sort F4_S4_L001_R1_001.fastq.gz.subread.BAM > F4.sorted.bam ; samtools sort F5_S5_L001_R1_001.fastq.gz.subread.BAM > F5.sorted.bam ; samtools sort F6_S6_L001_R1_001.fastq.gz.subread.BAM > F6.sorted.bam ; samtools sort F7_S7_L001_R1_001.fastq.gz.subread.BAM > F7.sorted.bam ; samtools sort F8_S8_L001_R1_001.fastq.gz.subread.BAM > F8.sorted.bam ; samtools sort F9_S9_L001_R1_001.fastq.gz.subread.BAM > F9.sorted.bam ; samtools sort G1_S13_L001_R1_001.fastq.gz.subread.BAM > G1.sorted.bam ; samtools sort G2_S14_L001_R1_001.fastq.gz.subread.BAM > G2.sorted.bam ; samtools sort G4_S16_L001_R1_001.fastq.gz.subread.BAM > G4.sorted.bam ; samtools sort G5_S17_L001_R1_001.fastq.gz.subread.BAM > G5.sorted.bam ; samtools sort G6_S18_L001_R1_001.fastq.gz.subread.BAM > G6.sorted.bam ; samtools index F11.sorted.bam ; samtools index F1.sorted.bam ; samtools index F2.sorted.bam ; samtools index F3.sorted.bam ; samtools index F4.sorted.bam ; samtools index F5.sorted.bam ; samtools index F6.sorted.bam ; samtools index F7.sorted.bam ; samtools index F8.sorted.bam ; samtools index F9.sorted.bam ; samtools index G1.sorted.bam ; samtools index G2.sorted.bam ; samtools index G4.sorted.bam ; samtools index G5.sorted.bam ; samtools index G6.sorted.bam ; bamCoverage -b F11.sorted.bam --normalizeUsing RPKM -o F11.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F1.sorted.bam --normalizeUsing RPKM -o F1.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F2.sorted.bam --normalizeUsing RPKM -o F2.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F3.sorted.bam --normalizeUsing RPKM -o F3.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F4.sorted.bam --normalizeUsing RPKM -o F4.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F5.sorted.bam --normalizeUsing RPKM -o F5.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F6.sorted.bam --normalizeUsing RPKM -o F6.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F7.sorted.bam --normalizeUsing RPKM -o F7.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F8.sorted.bam --normalizeUsing RPKM -o F8.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b F9.sorted.bam --normalizeUsing RPKM -o F9.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b G1.sorted.bam --normalizeUsing RPKM -o G1.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b G2.sorted.bam --normalizeUsing RPKM -o G2.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b G4.sorted.bam --normalizeUsing RPKM -o G4.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b G5.sorted.bam --normalizeUsing RPKM -o G5.bw --verbose --numberOfProcessors max/2 --binSize 1 ; bamCoverage -b G6.sorted.bam --normalizeUsing RPKM -o G6.bw --verbose --numberOfProcessors max/2 --binSize 1
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