From: Don Armstrong <don@donarmstrong.com>
Date: Tue, 26 May 2015 16:48:01 +0000 (-0700)
Subject: compress fastq
X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=2bc6dbafa8fd81f5207c778b165c5b7617168bb7;hp=98affeec50d3a50371d11dec2b691f68a2939893;p=uiuc_igb_scripts.git

compress fastq
---

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;