#!/bin/bash
PATH=/data/results/tools/samtools/samtools-0.1.19:/data/results/tools/align/bowtie2-2.2.8:/data/results/tools/align/tophat-2.1.1.Linux_x86_64:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/mnt/fix/b/Elixir/metabolomics/solvers/gurobi801/linux64/bin:/mnt/fix/b/Elixir/metabolomics/solvers/gurobi801/linux64/bin; export PATH
echo "Using tophat2 installation at"
which tophat2
tophat --version
echo "Using bowtie installation at"
which bowtie2
bowtie2 --version
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3   --no-novel-juncs --output-dir tophat_019 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts --GTF /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Annotation/Archives/archive-2015-07-17-14-33-26/Genes/genes.gtf  /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.GK3R188-Wt1.IonXpress_019.fastq &> 019.tophat-mm10.log
cd tophat_019;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_032 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.MV3R11-NKT2-3.IonXpress_032.fastq &> 032.tophat-mm10.log
cd tophat_032;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_035 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.MV3R14-NKT17-3.IonXpress_035.fastq &> 035.tophat-mm10.log
cd tophat_035;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_038 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.MV3R17-DPpre-3.IonXpress_038.fastq &> 038.tophat-mm10.log
cd tophat_038;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_011 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.MV3R2-ST0-2.IonXpress_011.fastq &> 011.tophat-mm10.log
cd tophat_011;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_045 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.MV3R20-DPpost-3.IonXpress_045.fastq &> 045.tophat-mm10.log
cd tophat_045;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_048 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.MV3R23-CD4-3.IonXpress_048.fastq &> 048.tophat-mm10.log
cd tophat_048;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_026 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.MV3R5-ST1-3.IonXpress_026.fastq &> 026.tophat-mm10.log
cd tophat_026;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;
/data/results/tools/align/tophat-2.1.1.Linux_x86_64/tophat2 -p 10 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3    --no-novel-juncs --output-dir tophat_029 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/mm10/mRNA/transcripts /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome R_2018_07_27_12_27_12_user_IONAS-405-DrMylonis_MV-GKlab_180727_IM3R1-6_GK3R188_MV3R.MV3R8-NKT1-3.IonXpress_029.fastq &> 029.tophat-mm10.log
cd tophat_029;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 10 --mm -x /data/results/reference/mmu/mm10/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/genome -U unmapped.fastq  | /data/results/tools/samtools/samtools-0.1.19/samtools view -uhS -F4 - | /data/results/tools/samtools/samtools-0.1.19/samtools sort - unmapped_remap; rm unmapped.fastq; samtools merge merged.bam  accepted_hits.bam unmapped_remap.bam; /data/results/tools/samtools/mysamtools-0.1.19/samtools sort  -@ 10 -n merged.bam sort; rm merged.bam; rm unmapped_remap.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/mm10/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;