diff expression_calculator/expression.sh @ 0:27ebc30a2024 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/expression_calculator/expression.sh	Wed Apr 18 03:35:12 2018 -0400
@@ -0,0 +1,37 @@
+#!/bin/bash
+
+if [ "$#" -ne 1 ]; then
+ echo "[usage:] expression.sh bam.file"
+ exit 1;
+fi
+
+INPUT_BAM=$1
+SAMPLE_ID="sample"
+SAMTOOLS=$GALAXY_HOME/package/DAUMSOFT/RNA-seq/Normalization/samtools
+HTSEQ_COUNT=$GALAXY_HOME/package/DAUMSOFT/RNA-seq/Normalization/htseq-count
+GTF=$GALAXY_HOME/package/DAUMSOFT/RNA-seq/Normalization/gencode.v22.annotation.gtf
+EXPRESSION_R=$GALAXY_HOME/package/DAUMSOFT/RNA-seq/Normalization/expression.r
+
+HTSEQ_COUNT_OUT=./$SAMPLE_ID".htseq-count.out"
+EXPRESSION_OUT=./out
+EXPRESSION_OUT_TMP=./out_tmp
+
+rm -rf  $EXPRESSION_OUT
+rm -rf  $EXPRESSION_OUT_TMP
+
+mkdir $EXPRESSION_OUT
+mkdir $EXPRESSION_OUT_TMP
+
+
+$SAMTOOLS view -F 4 $INPUT_BAM |
+$HTSEQ_COUNT \
+-m intersection-nonempty \
+-i gene_id \
+-r pos \
+-s no \
+- $GTF   > $HTSEQ_COUNT_OUT
+
+Rscript $EXPRESSION_R  $HTSEQ_COUNT_OUT 
+
+mv $EXPRESSION_OUT_TMP/$SAMPLE_ID".txt" $EXPRESSION_OUT/ 
+