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Solution
Solution
Warning
titleSubmit to the TACC queue

Move into your scratch directory and create a new directory:

Code Block
cds
mkdir day2
cd day2

Then create a commands file with the commands below and use launcher_creator.py followed by qsub to run them.

  1. Mapping
    1. For BWA, the commands are:
      Code Block
      titleONE LINE command for ALL bwa operations
      module load bwa; bwa aln $BI/ngs_course/human_variation/ref/hs37d5.fa $BI/ngs_course/human_variation/allseqs_R1.fastq > r1.sai && bwa aln $BI/ngs_course/human_variation/ref/hs37d5.fa $BI/ngs_course/human_variation/allseqs_R2.fastq > r2.sai && bwa sampe $BI/ngs_course/human_variation/ref/hs37d5.fa r1.sai r2.sai $BI/ngs_course/human_variation/allseqs_R1.fastq $BI/ngs_course/human_variation/allseqs_R1.fastq > test.sam
    2. For bowtie2:
      Code Block
      titleOne-line command for bowtie
      module load bowtie/2.0.0b6; bowtie2 -t -x $BI/ngs_course/human_variation/ref/hs37d5_bowtie2 -1 $BI/ngs_course/human_variation/allseqs_R1.fastq -2 $BI/ngs_course/human_variation/allseqs_R1R2.fastq   -S test.sam
  2. Convert, sort, and index output:
    Code Block
    titleOne-line command for samtools
    samtools view -S -b test.sam > test.bam && samtools sort test.bam test.sorted && samtools index test.sorted.bam

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