Update 1_MappingtoHuman

cd644fd8 · jlamanna9 · GitHub · 0362aeb9 · cd644fd8
Unverified Commit cd644fd8 authored 4 years ago by jlamanna9 Committed by GitHub 4 years ago
--- a/1_MappingtoHuman
+++ b/1_MappingtoHuman
 #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:/home/lamann10/lamann10/reference_files/IlluminaAdapter.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:20
+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 ./hg19.fasta trimmed_1A_S1_L001_R1_001.fastq > trimmed_1A_S1_L001_R1_001.sai
+./bwa-0.7.17/bwa aln ./hg19.fasta trimmed_1A_S1_L001_R2_001.fastq > trimmed_1A_S1_L001_R2_001.sai
+./bwa-0.7.17/bwa sampe ./hg19.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

-/home/lamann10/software/bwa-0.7.17/bwa aln /home/lamann10/scratch/cshl_2018/reference_files/mm10/mm10.fasta trimmed_1A_S1_L001_R1_001.fastq > trimmed_1A_S1_L001_R1_001.sai
+#Sort
+./samtools-1.8/samtools sort -o trimmed_1A_S1_L001_R1_001_sorted.bam trimmed_1A_S1_L001_R1_001.bam

-/home/lamann10/software/bwa-0.7.17/bwa aln /home/lamann10/scratch/cshl_2018/reference_files/mm10/mm10.fasta trimmed_1A_S1_L001_R2_001.fastq > trimmed_1A_S1_L001_R2_001.sai
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-/home/lamann10/software/bwa-0.7.17/bwa sampe /home/lamann10/scratch/cshl_2018/reference_files/mm10/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
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-/home/lamann10/software/samtools-1.8/samtools view -S -b trimmed_1A_S1_L001_R1_001.sam > trimmed_1A_S1_L001_R1_001.bam
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-/home/lamann10/software/samtools-1.8/samtools sort -o trimmed_1A_S1_L001_R1_001_sorted.bam trimmed_1A_S1_L001_R1_001.bam
-/home/lamann10/software/bedtools2/bin/bedtools bamtobed -i trimmed_1A_S1_L001_R1_001_sorted.bam > trimmed_1A_S1_L001_R1_001_sorted.bed
+#BamtoBed
+./bedtools bamtobed -i trimmed_1A_S1_L001_R1_001_sorted.bam > trimmed_1A_S1_L001_R1_001_sorted.bed