#!/bin/bash
PATH=/data/results/tools/align/tophat-2.0.10.Linux_x86_64:/data/results/tools/chipseq/ngsplot/bin:/data/results/tools/r/R-3.0.1/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games; export PATH
echo "Using tophat2 installation at"
which tophat2
tophat --version
PATH=/data/results/tools/align/bowtie2-2.1.0:/data/results/tools/chipseq/ngsplot/bin:/data/results/tools/r/R-3.0.1/bin:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games; export PATH
echo "Using bowtie installation at"
which bowtie2
bowtie2 --version
/data/results/tools/align/tophat-2.0.10.Linux_x86_64/tophat2 -p 8 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --output-dir tophat_011 --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_2014_06_24_05_42_51_user_ION-72-ITlab_MSRNAseq_140624_ITR19_ITR23..IonXpressRNA_011.fastq &> 011.tophat-mm9a.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 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-2.0.10.Linux_x86_64/tophat2 -p 8 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3  --output-dir tophat_005 --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_2014_06_24_05_42_51_user_ION-72-ITlab_MSRNAseq_140624_ITR19_ITR23.ITR19.IonXpressRNA_005.fastq &> 005.tophat-mm9a.log
cd tophat_005;/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 ..;