From 1c6418d2065b3be390d3e1d5229eb7f8cc03c6af Mon Sep 17 00:00:00 2001
From: jlamanna9 <41341179+jlamanna9@users.noreply.github.com>
Date: Tue, 16 Jun 2020 13:37:05 -0400
Subject: [PATCH] Create 2_MappingtoMouse

---
 2_MappingtoMouse | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 2_MappingtoMouse

diff --git a/2_MappingtoMouse b/2_MappingtoMouse
new file mode 100644
index 0000000..47d59fc
--- /dev/null
+++ b/2_MappingtoMouse
@@ -0,0 +1,14 @@
+#Trim
+java -jar ./Trimmomatic-0.36/trimmomatic-0.36.jar PE -phred33 1A_S1_L001_R1_001.fastq 1A_S1_L001_R2_001.fastq trimmed_1A_S1_L001_R1_001.fastq trimmed_U_1A_S1_L001_R1_001.fastq trimmed_1A_S1_L001_R2_001.fastq trimmed_U_1A_S1_L001_R2_001.fastq ILLUMINACLIP:./IlluminaAdapter.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:20
+
+#Align
+./bwa-0.7.17/bwa aln ./mm10.fasta trimmed_1A_S1_L001_R1_001.fastq > trimmed_1A_S1_L001_R1_001.sai
+./bwa-0.7.17/bwa aln ./mm10.fasta trimmed_1A_S1_L001_R2_001.fastq > trimmed_1A_S1_L001_R2_001.sai
+./bwa-0.7.17/bwa sampe ./mm10.fasta trimmed_1A_S1_L001_R1_001.sai trimmed_1A_S1_L001_R2_001.sai 1A_S1_L001_R1_001.fastq 1A_S1_L001_R2_001.fastq > trimmed_1A_S1_L001_R1_001.sam
+./samtools-1.8/samtools view -S -b trimmed_1A_S1_L001_R1_001.sam > trimmed_1A_S1_L001_R1_001.bam
+
+#Sort
+./samtools-1.8/samtools sort -o trimmed_1A_S1_L001_R1_001_sorted.bam trimmed_1A_S1_L001_R1_001.bam
+
+#BamtoBed
+./bedtools bamtobed -i trimmed_1A_S1_L001_R1_001_sorted.bam > trimmed_1A_S1_L001_R1_001_sorted.bed
-- 
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