convert standard analysis pipelines to use bam format natively

[erange.git] / docs / runStandardAnalysis.sh

diff --git a/docs/runStandardAnalysis.sh b/docs/runStandardAnalysis.sh
index aa5fe60588a30ceba6a65301db81b13ac4f6051f..830abea6ecec73a603597d0989e49763cc5f67bd 100755 (executable)
--- a/docs/runStandardAnalysis.sh
+++ b/docs/runStandardAnalysis.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 #
+# This is no longer supported.  It is recommended that the pythin script of the same name be used instead.
+#
 # runStandardAnalysis.sh
 # ENRAGE
 #
@@ -88,4 +90,4 @@ python $ERANGEPATH/geneMrnaCountsWeighted.py $1 $2.rds $2.expanded.rpkm $2.multi
 echo "python $ERANGEPATH/normalizeFinalExonic.py $2.rds $2.expanded.rpkm $2.multi.count $2.final.rpkm --multifraction --withGID --cache"
 python $ERANGEPATH/normalizeFinalExonic.py $2.rds $2.expanded.rpkm $2.multi.count $2.final.rpkm --multifraction --withGID --cache
 
-fi
\ No newline at end of file
+fi