From 2bc6dbafa8fd81f5207c778b165c5b7617168bb7 Mon Sep 17 00:00:00 2001
From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 09:48:01 -0700
Subject: [PATCH] compress fastq

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

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 4f75cf3..abcf486 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -11,7 +11,7 @@ function actually_run_the_alignment {
     module load cufflinks/2.2.1;
     module load samtools/0.1.18
     (cd $FROM_SRR_SRR;
-     fastq-dump ${FROM_SRR_SRR}.sra;
+     fastq-dump --gzip ${FROM_SRR_SRR}.sra;
      bwa mem -t ${CORES} $FROM_SRR_REF ${FROM_SRR_SRR}.fastq.gz | samtools view -b -o ${FROM_SRR_SRR}.bam;
      samtools sort ${FROM_SRR_SRR}.bam -o ${FROM_SRR_SRR}.sorted.bam -T temp
      cufflinks -p ${MAX_MEM} -G $FROM_SRR_GTF ${FROM_SRR_SRR}.sorted.bam;
-- 
2.39.2