Mercurial > repos > davidvanzessen > mutation_analysis

diff wrapper.sh @ 41:1b45c7d7d941 draft

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Uploaded
author davidvanzessen
date Mon, 02 Nov 2015 09:20:13 -0500
parents e022c21f8c47
children 7304b91757a8
line wrap: on
line diff
--- a/wrapper.sh	Mon Nov 02 07:10:36 2015 -0500
+++ b/wrapper.sh	Mon Nov 02 09:20:13 2015 -0500
@@ -24,6 +24,7 @@
 fi
 
 cat $PWD/files/*/1_* > $PWD/summary.txt
+cat $PWD/files/*/3_* > $PWD/sequences.txt
 cat $PWD/files/*/6_* > $PWD/junction.txt
 cat $PWD/files/*/7_* > $PWD/mutationanalysis.txt
 cat $PWD/files/*/8_* > $PWD/mutationstats.txt
@@ -54,7 +55,7 @@
 
 
 echo "merging"
-Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/junction.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique
+Rscript $dir/merge_and_filter.r $PWD/summary.txt $PWD/sequences.txt $PWD/mutationanalysis.txt $PWD/mutationstats.txt $PWD/hotspots.txt $outdir/identified_genes.txt $outdir/merged.txt $outdir/unmatched.txt $method $functionality $unique
 
 genes="ca,ca1,ca2,cg,cg1,cg2,cg3,cg4,cm"
 echo "R mutation analysis"