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  • What new files were created by these commands?
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    Check that
    Code Block
    titleList the contents of the output directory
    ls samtools_bowtie
    
    Code Block
    titleExpected output
    NC_012967.1.fasta      SRR030257.bcf         SRR030257.sorted.bam.bai
    NC_012967.1.fasta.fai  SRR030257.sam
    SRR030257.bam          SRR030257.sorted.bam
    
  • Why didn't we name the output SRR030257.sorted.bam in the samtools sort command?
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    Answer...
    Answer...

    Samtools appends an extra .bam to whatever we put here, so it would have created SRR030257.sorted.bam.bam, and we would have had to make a joke about the Flintstones.

  • Can you guess what a *.bai file is?
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    Answer...
    Answer...

    Sure enough, it's the index file for the BAM file.

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