#!/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:/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-2.1.1.Linux_x86_64/tophat2 -p 3 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --no-novel-juncs  --output-dir tophat_008 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.PHR16-CON2.IonXpress_008.fastq &> 008.tophat-mm9a.log
cd tophat_008;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 3 --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  -@ 3 -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 3 --read-mismatches 3 --read-gap-length 3 --read-edit-dist 3 --no-novel-juncs  --output-dir tophat_009 --keep-fasta-order --transcriptome-index=/data/results/reference/hg19/mRNA/transcripts /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.PHR17-DOX1.IonXpress_009.fastq &> 009.tophat-mm9a.log
cd tophat_009;/data/results/tools/formats/bam2fastq-1.1.0/bam2fastq -o unmapped.fastq -q unmapped.bam;  bowtie2 --local --very-sensitive-local -p 3 --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  -@ 3 -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 ..;