compress fastq

diff --git a/fpkm_from_srr b/fpkm_from_srr
index 4f75cf370bacd0f2296d5a28d16f43c572bcd327..abcf486f7cf479c2dca4e330af1b362e37e43d0f 100755 (executable)
--- 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;