#!/bin/bash
PATH=/data/results/tools/align/tophat-2.0.10.Linux_x86_64:/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/.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
PATH=/data/results/tools/align/bowtie2-2.1.0:/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/.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 bowtie installation at"
which bowtie2
bowtie2 --version
echo R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC51-ChIRP-Input.IonXpress_020.fastq
mkdir bowtie2_020; cd bowtie2_020; bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U ../R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC51-ChIRP-Input.IonXpress_020.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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
echo R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC52-ChIRP-ODD.IonXpress_021.fastq
mkdir bowtie2_021; cd bowtie2_021; bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U ../R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC52-ChIRP-ODD.IonXpress_021.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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
echo R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC53-ChIRP-EVEN.IonXpress_022.fastq
mkdir bowtie2_022; cd bowtie2_022; bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U ../R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC53-ChIRP-EVEN.IonXpress_022.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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
echo R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC54-ChIRP-LacZ.IonXpress_023.fastq
mkdir bowtie2_023; cd bowtie2_023; bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U ../R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC54-ChIRP-LacZ.IonXpress_023.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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
echo R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC55-MCF-Input.IonXpress_024.fastq
mkdir bowtie2_024; cd bowtie2_024; bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U ../R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC55-MCF-Input.IonXpress_024.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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
echo R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC56-MCF-Acl2.IonXpress_025.fastq
mkdir bowtie2_025; cd bowtie2_025; bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U ../R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC56-MCF-Acl2.IonXpress_025.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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
echo R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC57-MCF-bcat.IonXpress_026.fastq
mkdir bowtie2_026; cd bowtie2_026; bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U ../R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC57-MCF-bcat.IonXpress_026.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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;
echo R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC58-MCF-TCF4.IonXpress_027.fastq
mkdir bowtie2_027; cd bowtie2_027; bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U ../R_2017_08_02_13_06_24_user_IONAS-362-KEELPNO_PHlab_DrApid_170802_KLPNC1-3_PHC51-58_YAbR24reseq_.PHC58-MCF-TCF4.IonXpress_027.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/hg19/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa.fai - > sort_uniq.bam; cd ..;