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  • Expand
    titleWhat new files were created by these commands?
    Code Block
    languagebash
    titleList the contents of the output directory
    ls
samtools_bowtie2
    Code Block
    titleExpected output
    NC_012967.1.fasta      SRR030257.sorted.bam.bai
NC_012967.1.fasta.fai  SRR030257.sam
SRR030257.bam          SRR030257.sorted.bam
  • Expand
    titleWhy didn't we name the output SRR030257.sorted.bam in the samtools sort command?

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

  • Expand
    titleCan you guess what a *.bai file is?

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

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Code Block
languagebash
titleIf you have done any of the optional other mapping tutorials, consider the following comparisons. Remember the use of cp -i (or cp -n on some newer linux versions) is useful to make sure you don't overwrite any existing files.
mkdir comparison
cp -ni samtools_bowtie2/SRR030257.vcf comparison/bowtie2.vcf
cp -ni samtools_bwa/SRR030257.vcf comparison/bwa.vcf
cp -ni samtools_bowtie/SRR030257.vcf comparison/bowtie.vcf
cd comparison

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