Mercurial > repos > mingchen0919 > gtg_star_demo

diff 1-index-genome.sh @ 0:a1448d1f2ee4 draft

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planemo upload
author mingchen0919
date Wed, 20 Jun 2018 10:24:45 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1-index-genome.sh	Wed Jun 20 10:24:45 2018 -0400
@@ -0,0 +1,11 @@
+# create genome directory for genome indices.
+mkdir -p ${X_d}/genomeDir
+
+STAR \
+  --runMode genomeGenerate \
+  --genomeDir ${X_d}/genomeDir \
+  --genomeFastaFiles $( echo ${X_A} | sed 's/,/ /g' ) \
+  --sjdbGTFfile ${X_B} \
+  --sjdbOverhang ${X_C} \
+  > genome-indexing.log.txt 2>&1
+  
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