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Update TU502_2012_SNPAnalysis
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@gwc32007
gwc32007 authored Feb 19, 2019
1 parent 34d4002 commit 108a52e
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion TU502_2012_SNPAnalysis
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Expand Up @@ -22,7 +22,7 @@ time bwa index /scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta
cd $PBS_O_WORKDIR

module load BWA/0.7.17-foss-2016b
time bwa mem -M -t 16 /scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta /scratch/gwc32007/crypto_fastq/TU502_2012/SRR1015747_1.fastq /scratch/gwc32007/crypto_fastq/TU502_2012/SRR1015747_2.fastq > /scratch/gwc32007/fastq_alignments/TU502_2012_aln.sam
time bwa mem -M -t 16 /scratch/gwc32007/crypto_genomes/cparvum_iowaII_genome.fasta /scratch/gwc32007/crypto_fastq/TU502_2012/SRR1015747_1.fastq.gz /scratch/gwc32007/crypto_fastq/TU502_2012/SRR1015747_2.fastq.gz > /scratch/gwc32007/fastq_alignments/TU502_2012_aln.sam

#converts the .sam file to a more condensed .bam file

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