From a32983b65fbbb0a8f052cc1e125f40f686a5b509 Mon Sep 17 00:00:00 2001
From: jlamanna9 <41341179+jlamanna9@users.noreply.github.com>
Date: Tue, 16 Jun 2020 14:37:40 -0400
Subject: [PATCH] Create 3_GenerateReadsPer500kb

---
 3_GenerateReadsPer500kb | 12 ++++++++++++
 1 file changed, 12 insertions(+)
 create mode 100644 3_GenerateReadsPer500kb

diff --git a/3_GenerateReadsPer500kb b/3_GenerateReadsPer500kb
new file mode 100644
index 0000000..e86f746
--- /dev/null
+++ b/3_GenerateReadsPer500kb
@@ -0,0 +1,12 @@
+#MarkDuplicates
+java -jar ./picard.jar MarkDuplicates I= trimmed_1A_S1_L001_R1_001_sorted.bam O= trimmed_1A_S1_L001_R1_001_sorted_rmdup.bam M= trimmed_1A_S1_L001_R1_001_sorted_rmdup.metrics ASSUME_SORTED=true VALIDATION_STRINGENCY=LENIENT REMOVE_DUPLICATES=true
+
+#RemoveDuplicates
+./samtools-1.8/samtools index trimmed_1A_S1_L001_R1_001_sorted_rmdup.bam
+./samtools-1.8/samtools view -bu trimmed_1A_S1_L001_R1_001_sorted_rmdup.bam | ./bamToBed -i stdin > trimmed_1A_S1_L001_R1_001_sorted_rmdup.bed
+
+#GenerateReadsPer500kbBin
+cat trimmed_1A_S1_L001_R1_001_sorted_rmdup.bed | sed -e "s/-1/0/g" | awk '{print $1"\t"$2"\t"$2+1}' > trimmed_1A_S1_L001_R1_001_sorted_rmdup_onebasereads.bed
+./intersectBed -a trimmed_1A_S1_L001_R1_001_sorted_rmdup_onebasereads.bed -b ./b37.40mer.nonUniqSites.merged.bed  -v > trimmed_1A_S1_L001_R1_001_sorted_rmdup_onebasereads_winIntersect.bed
+./coverageBed -b trimmed_1A_S1_L001_R1_001_sorted_sorted_rmdup_onebasereads_winIntersect.bed -a ./all.window.40mer.b37.map.500kb.bed -counts > trimmed_1A_S1_L001_R1_001_sorted_rmdup_onebasereads_winIntersect_500kb.cov
+cat trimmed_1A_S1_L001_R1_001_sorted_rmdup_onebasereads_winIntersect_500kb.cov | sed -e "s/X/23/g" | sed -e "s/Y/24/g" | sort -k 1 -n -k 2 -n > trimmed_1A_S1_L001_R1_001_sorted_rmdup_onebasereads_winIntersect_500kb_SORT.cov
-- 
GitLab