#!/bin/bash
#PATH=/data/results/tools/align/tophat-2.0.10.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
PATH=/data/results/tools/align/bowtie2-2.2.8:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games; export PATH
echo "Using bowtie installation at"
which bowtie2
bowtie2 --version
mkdir bowtie2_002; cd bowtie2_002;  bowtie2 --local --very-sensitive-local -p 6 --mm -x /data/results/reference/mmu/Mus_musculus/UCSC/mm9/Sequence/Bowtie2Index2/genome -U ../R_2016_04_19_11_40_37_user_IONAS-288-ITlab-PHlab-DrSkretas_160419_ITC109_PHR16-17_GSKP4-5.ITC109-wt2Ser2.IonXpress_002.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  -@ 6 -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 ..;