X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fpkm_from_srr;h=abcf486f7cf479c2dca4e330af1b362e37e43d0f;hb=2bc6dbafa8fd81f5207c778b165c5b7617168bb7;hp=a7ab6e0a4ef9c03c818c9737f1c0a810cc7b87f8;hpb=13f54c1d3fd7c8ea0294f0b6ae81eedfca6e1ea5;p=uiuc_igb_scripts.git

diff --git a/fpkm_from_srr b/fpkm_from_srr
index a7ab6e0..abcf486 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -9,8 +9,9 @@ function actually_run_the_alignment {
     module load sratoolkit/2.3.5-2;
     module load bwa/0.7.10;
     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;