#!/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:/home/reczko/perl5/bin:/home/reczko/.opam/system/bin:/data/results/tools/align/blast/ncbi-blast-2.2.29+/bin:/home/reczko/a/tools/rna/structural-motifs/CMfinder_0.2/bin:/home/reczko/a/tools/libs/www/firefox:/home/reczko/a/tools/libs/boost/bin:/data/results/tools/ml/torch/torch/install/bin:/data/results/tools/chipseq/ngsplot/bin:/data/results/tools/bedtools/BEDTools-Version-2.14.3/bin:/data/results/tools/samtools/mysamtools-0.1.19:/data/results/tools/denovo/gene-finding/snap:/data/results/tools/denovo/gene-finding/exonerate-2.2.0-x86_64/bin:/data/results/tools/denovo/gene-finding/augustus-3.0.3/bin:/data/results/tools/denovo/gene-finding/augustus-3.0.3/scripts:/data/results/tools/align/blast/ncbi-blast-2.2.29+/bin:/data/results/tools/denovo/repeats/RepeatMasker:/data/results/tools/protein/tmhmm-2.0c/bin:/data/results/tools/align/rsem/rsem-1.2.15:/data/results/tools/chipseq/ngsplot/bin:/home/reczko/a/tools/libs/java/jdk1.8.0_66/bin:/home/reczko/a/tools/ml/tensorflow/bazel/output:/usr/lib/jvm/java-7-openjdk-amd64/jre/bin:/usr/java/jre1.8.0_45/bin:/data/results/tools/samtools/samtools-1.0:/data/results/tools/align/bowtie-1.1.0:/data/results/tools/r/R-3.0.1/bin:/data/results/tools/ml/torch/torch/install/bin:/home/reczko/bin:/home/reczko/perl5/bin:/home/reczko/.opam/system/bin:/data/results/tools/align/blast/ncbi-blast-2.2.29+/bin:/home/reczko/a/tools/rna/structural-motifs/CMfinder_0.2/bin:/home/reczko/a/tools/libs/www/firefox:/home/reczko/a/tools/libs/boost/bin:/data/results/tools/ml/torch/torch/install/bin:/data/results/tools/chipseq/ngsplot/bin:/data/results/tools/bedtools/BEDTools-Version-2.14.3/bin:/data/results/tools/samtools/mysamtools-0.1.19:/data/results/tools/denovo/gene-finding/snap:/data/results/tools/denovo/gene-finding/exonerate-2.2.0-x86_64/bin:/data/results/tools/denovo/gene-finding/augustus-3.0.3/bin:/data/results/tools/denovo/gene-finding/augustus-3.0.3/scripts:/data/results/tools/align/blast/ncbi-blast-2.2.29+/bin:/data/results/tools/denovo/repeats/RepeatMasker:/data/results/tools/protein/tmhmm-2.0c/bin:/data/results/tools/align/rsem/rsem-1.2.15:/data/results/tools/chipseq/ngsplot/bin:/home/reczko/a/tools/libs/java/jdk1.8.0_66/bin:/home/reczko/a/tools/ml/tensorflow/bazel/output:/usr/lib/jvm/java-7-openjdk-amd64/jre/bin:/usr/java/jre1.8.0_45/bin:/data/results/tools/samtools/samtools-1.0:/data/results/tools/align/bowtie-1.1.0:/data/results/tools/r/R-3.0.1/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/script:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/util:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/bin/x86_64:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/script:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/util:/data/results/tools/rna/protein-coding-potential/lncRScan-SVM_v1.0.1/executable/bin/x86_64; 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_003 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1IonXpress_003.fastq &> 003.tophat-mm9a.log
cd tophat_003;/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_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1IonXpress_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_041 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1IonXpress_041.fastq &> 041.tophat-mm9a.log
cd tophat_041;/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_042 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1IonXpress_042.fastq &> 042.tophat-mm9a.log
cd tophat_042;/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_043 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1IonXpress_043.fastq &> 043.tophat-mm9a.log
cd tophat_043;/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_044 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1IonXpress_044.fastq &> 044.tophat-mm9a.log
cd tophat_044;/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_047 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1IonXpress_047.fastq &> 047.tophat-mm9a.log
cd tophat_047;/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_048 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1IonXpress_048.fastq &> 048.tophat-mm9a.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/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_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.MT3R19-lq-iP2.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_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.MT3R20-lq-iP4.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_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.MT3R21-lq-iP7.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_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.MT3R22-iP13.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 ..;
/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_024 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.MT3R24-hD10.IonXpress_024.fastq &> 024.tophat-mm9a.log
cd tophat_024;/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_031 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.PH3R41-MCas12-Con1.IonXpress_031.fastq &> 031.tophat-mm9a.log
cd tophat_031;/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_032 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.PH3R42-MCas12-Con2.IonXpress_032.fastq &> 032.tophat-mm9a.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/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_033 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.PH3R43-MCas12-Con3.IonXpress_033.fastq &> 033.tophat-mm9a.log
cd tophat_033;/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_034 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.PH3R44-MCas12-Dox1.IonXpress_034.fastq &> 034.tophat-mm9a.log
cd tophat_034;/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_035 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.PH3R45-MCas12-Dox2.IonXpress_035.fastq &> 035.tophat-mm9a.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/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_036 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2017_12_18_17_11_17_user_IONAS-375-DrTokameh_PHlab_YK_171218_MT3R19-23_PH3R41-46_YKR1.PH3R46-MCas12-Dox3.IonXpress_036.fastq &> 036.tophat-mm9a.log
cd tophat_036;/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 ..;