#!/bin/bash
PATH=/data/results/tools/align/tophat-2.0.10.Linux_x86_64:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games; export PATH
echo "Using tophat2 installation at"
which tophat2
tophat --version
PATH=/data/results/tools/align/bowtie2-2.1.0:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games; export PATH
echo "Using bowtie installation at"
which bowtie2
bowtie2 --version
mkdir bowtie2_005; cd bowtie2_005;  bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -U ../R_2014_05_21_05_30_33_user_ION-61-ITLab_MSChIP_140521_A-B-D-E1.A1.IonXpress_005.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - merged ; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 8 -n merged.bam sort; rm merged.bam; samtools view sort.bam   | awk -f /data/results/tools/formats/sam-remove-read-multimaps-to-same-location2.awk | samtools view -bt /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
mkdir bowtie2_006; cd bowtie2_006;  bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -U ../R_2014_05_21_05_30_33_user_ION-61-ITLab_MSChIP_140521_A-B-D-E1.B1.IonXpress_006.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - merged ; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 8 -n merged.bam sort; rm merged.bam; samtools view sort.bam   | awk -f /data/results/tools/formats/sam-remove-read-multimaps-to-same-location2.awk | samtools view -bt /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
mkdir bowtie2_007; cd bowtie2_007;  bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -U ../R_2014_05_21_05_30_33_user_ION-61-ITLab_MSChIP_140521_A-B-D-E1.D1.IonXpress_007.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - merged ; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 8 -n merged.bam sort; rm merged.bam; samtools view sort.bam   | awk -f /data/results/tools/formats/sam-remove-read-multimaps-to-same-location2.awk | samtools view -bt /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
mkdir bowtie2_008; cd bowtie2_008;  bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome -U ../R_2014_05_21_05_30_33_user_ION-61-ITLab_MSChIP_140521_A-B-D-E1.E1.IonXpress_008.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - merged ; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 8 -n merged.bam sort; rm merged.bam; samtools view sort.bam   | awk -f /data/results/tools/formats/sam-remove-read-multimaps-to-same-location2.awk | samtools view -bt /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;