#!/bin/bash
PATH=/data/results/tools/align/bowtie2-2.2.3:/data/results/tools/align/tophat-2.0.12.Linux_x86_64:/home/reczko/ocamlbrew/ocaml-4.01.0/.opam/system/bin:/home/reczko/ocamlbrew/ocaml-4.01.0/.opam/system/bin:/home/reczko/ocamlbrew/ocaml-4.01.0/bin:/data/results/tools/chipseq/macs/bin:/data/results/tools/bedtools/BEDTools-Version-2.14.3/bin:/data/results/tools/chipseq/ngsplot/bin:/data/results/tools/r/R-3.1.2/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games; 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-2.0.12.Linux_x86_64/tophat2 -p 8 --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/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts --GTF /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Annotation/Genes/genes.gtf /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome R_2015_01_27_12_20_40_user_ION-130-GKlab_RNAseq_150127_GKR3-4.GKR3-wt2early.IonXpressRNA_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 8 --mm -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/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  -@ 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 ..;
/data/results/tools/align/tophat-2.0.12.Linux_x86_64/tophat2 -p 8 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --no-novel-juncs  --output-dir tophat_004 --keep-fasta-order --transcriptome-index=/data/results/reference/mmu/Mus_musculus/UCSC/mm9/mRNA/transcripts /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index/genome R_2015_01_27_12_20_40_user_ION-130-GKlab_RNAseq_150127_GKR3-4.GKR4-DARE2early.IonXpressRNA_004.fastq &> 004.tophat-mm9a.log
cd tophat_004;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 8 --mm -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/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  -@ 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 ..;