diff --git a/1_MappingtoHuman b/1_MappingtoHuman
index 922dd34b8b718ee964b4b0de4ee16315c4083d2d..be0d009ba3be07b3fd93b63b2b2cf1a12c6cdcab 100644
--- a/1_MappingtoHuman
+++ b/1_MappingtoHuman
@@ -1,16 +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:/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
-
-
-/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
-
-
-/home/lamann10/software/samtools-1.8/samtools view -S -b trimmed_1A_S1_L001_R1_001.sam > trimmed_1A_S1_L001_R1_001.bam
-
-/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