changes.mady.by.user Scott Patrick Hunicke-Smith
Saved on Aug 20, 2012
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Move into your scratch directory and create a new directory:
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.
commands
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
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
samtools view -S -b test.sam > test.bam && samtools sort test.bam test.sorted && samtools index test.sorted.bam