X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=fpkm_from_srr;h=27cad20bcacb01eb506f6c35ae1de0ea579d05f0;hb=0e5f3745f8f445db4cc77967c3baa0ed25362e97;hp=abcf486f7cf479c2dca4e330af1b362e37e43d0f;hpb=2bc6dbafa8fd81f5207c778b165c5b7617168bb7;p=uiuc_igb_scripts.git

diff --git a/fpkm_from_srr b/fpkm_from_srr
index abcf486..27cad20 100755
--- a/fpkm_from_srr
+++ b/fpkm_from_srr
@@ -9,7 +9,7 @@ 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
+    module load samtools/1.0;
     (cd $FROM_SRR_SRR;
      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;