--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/filter_bam.bash	Sat Apr 28 15:07:26 2018 -0400
@@ -0,0 +1,35 @@
+#Requires bam files and bed file containing coordinates of peaks of interest
+#Generates filtered bams and library size file to upload into Galaxy
+
+#required arguements:
+#($1): bam file
+#($2): bed file containing regions of interest
+
+#Usage: filter_bam /pathtofolder/ qPCR_peaks.bed
+
+#outputs:
+#Filtered bam files containing reads in regions of interest
+#read_counts: txt file containing number of mapped reads in each bam file, used for normalization
+
+bam_file=$1
+peak_file=$2
+chrom_sizes=$3
+ext_peak_file=$4
+filtered_bam_file=$5
+read_counts=$6
+name=$7
+
+bedtools slop -i $peak_file -g $chrom_sizes -b 2000 | sort -k1,1 -k2,2n - > $ext_peak_file
+
+samtools index $bam_file
+
+samtools view -c -F 1284 $bam_file > count
+echo $name > name
+paste name count > $read_counts
+
+#create bed file of fragments for each bam file
+
+samtools view -b -L $ext_peak_file $bam_file > $filtered_bam_file
+
+rm name
+rm count