--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/window_coverage.bash	Sat Apr 28 15:07:26 2018 -0400
@@ -0,0 +1,67 @@
+#!/bin/bash
+
+#Requires bam files and bed file containing coordinates of peaks of interest
+#Determines regions within peaks where included fragement coverage best correlates
+#with total read count under peak.  Exports regions as bed file.
+
+#required arguements:
+#($1): series of bam files
+#($2): file names of bam files
+#($3): window bed file
+#($4): percent of window fragments must cover, default is 0.9
+#($5): output coverage file
+#($6): output spanning fragment coverage file
+
+#Usage: ATAC_qPCR_regions.bash bam_series name_list qPCR_windows.bed 0.9 combined.o.bed.coverage combined.f9.bed.coverage
+
+bam_series=$1
+name_list=$2
+qPCR_windows=$3
+percent_overlap=${4:-0.9}
+combined_o=$5
+combined_f9=$6
+
+COUNTER=0
+echo $bam_series |tr , '\n' > bam_series.txt
+echo $name_list | tr , '\n' > name_list.txt
+paste name_list.txt bam_series.txt > bam_name_list.txt
+sort -k1 bam_name_list.txt > sorted_bam_name_list.txt
+cut -f 2 sorted_bam_name_list.txt > sorted_bam_list.txt
+
+cat sorted_bam_list.txt | while read file
+do
+
+#create bed file of fragments for each bam file
+
+samtools sort -n -o - $file | samtools fixmate - - | bamToBed -i - -bedpe | cut -f 1,2,6 > "${file}".includeinsert.bed
+
+#determine window coverage for each bam file
+#combined_o: Total reads in peak/window
+#combined_f9: Spanning reads in window
+
+if [ $COUNTER -eq 0 ]
+then
+coverageBed -a $qPCR_windows -b $file | cut -f 1,2,3,4,5 > $combined_o
+coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 1,2,3,4,5 > $combined_f9
+
+else
+coverageBed -a $qPCR_windows -b $file | cut -f 5 > temp.o.bed.coverage
+coverageBed -a $qPCR_windows -b "${file}".includeinsert.bed -f $percent_overlap | cut -f 5 > temp.f9.bed.coverage
+paste $combined_o temp.o.bed.coverage > combined.temp.o.bed.coverage
+mv combined.temp.o.bed.coverage $combined_o
+paste $combined_f9 temp.f9.bed.coverage > combined.temp.f9.bed.coverage
+mv combined.temp.f9.bed.coverage $combined_f9
+
+rm temp.o.bed.coverage
+rm temp.f9.bed.coverage
+
+fi
+
+rm "${file}.includeinsert.bed"
+
+let COUNTER=COUNTER+1
+
+done
+
+
+rm *.txt