From 108a52e8158fd41f6acef233dda580c7f6727438 Mon Sep 17 00:00:00 2001
From: gwc32007 <43821509+gwc32007@users.noreply.github.com>
Date: Tue, 19 Feb 2019 11:44:25 -0500
Subject: [PATCH] Update TU502_2012_SNPAnalysis

---
 TU502_2012_SNPAnalysis | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/TU502_2012_SNPAnalysis b/TU502_2012_SNPAnalysis
index 441dbfc..389edbc 100644
--- a/TU502_2012_SNPAnalysis
+++ b/TU502_2012_SNPAnalysis
@@ -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