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28 lines
458 B
Bash
28 lines
458 B
Bash
#!/bin/bash
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fastqc Bacteria_GATTACA_L001_R1_001.fastq
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cutadapt \
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-a file:Adapter_Sequence.fasta \
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-o trimmed.fastq \
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Bacteria_GATTACA_L001_R1_001.fastq
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fastqc trimmed.fastq
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mkdir star_index
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STAR \
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--runMode genomeGenerate \
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--genomeDir ./star_index \
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--genomeFastaFiles rDNA_sequence.fasta \
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--genomeSAindexNbases 3
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STAR \
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--genomeDir ./star_index \
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--readFilesIn ./trimmed.fastq
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featureCounts \
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-a rDNA.gtf \
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-t CDS \
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-o counts.txt \
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Aligned.out.sam
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