#!/bin/bash
PATH=$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:/home/reczko/anaconda3/bin:/home/reczko/anaconda3/condabin:/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
tophat2 --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_015 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts --GTF /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2012-03-09-03-24-41/Genes/genes.gtf  /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R25_261-2_Ctrl_tr.IonXpress_015.fastq &> 015.tophat-mm9a.log
cd tophat_015;/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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/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_016 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R26_272-2_Ctrl_tr.IonXpress_016.fastq &> 016.tophat-mm9a.log
cd tophat_016;/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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/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_017 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R27_283-2_Ctrl_tr.IonXpress_017.fastq &> 017.tophat-mm9a.log
cd tophat_017;/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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/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_018 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R28_285-288_Ctrl_tr.IonXpress_018.fastq &> 018.tophat-mm9a.log
cd tophat_018;/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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/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_019 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R29_261-5_Cre_tr.IonXpress_019.fastq &> 019.tophat-mm9a.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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/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_020 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R30_272-3_Cre_tr.IonXpress_020.fastq &> 020.tophat-mm9a.log
cd tophat_020;/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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/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_021 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R31_343-4_Ctrl_untr.IonXpress_021.fastq &> 021.tophat-mm9a.log
cd tophat_021;/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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/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_022 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R32_343-5_Ctrl_untr.IonXpress_022.fastq &> 022.tophat-mm9a.log
cd tophat_022;/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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/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_023 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2021_12_07_14_07_32_user_IONAS-514-VKlab-PMN_211207_VK3R25-33_PMN165-168.VK3R33_348-3_Ctrl_untr.IonXpress_023.fastq &> 023.tophat-mm9a.log
cd tophat_023;/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/hg19/Homo_sapiens/UCSC/hg19/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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; rm sort.bam; cd ..;