#!/bin/bash
PATH=/data/results/tools/align/bowtie2-2.1.0:/mnt/raid/tools/align/tophat-2.0.9.Linux_x86_64:/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/opt/dell/srvadmin/bin; export PATH
echo "Using bowtie installation at"
which bowtie2
bowtie2 --version
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2014_02_05_06_10_30_user_ION-32-PHLab_140205_ChIRP-seq_CPH1-4.CPH1.IonXpress_005.fastq |samtools view -Sb - > 005.bam 2> 005_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2014_02_05_06_10_30_user_ION-32-PHLab_140205_ChIRP-seq_CPH1-4.CPH2.IonXpress_006.fastq |samtools view -Sb - > 006.bam 2> 006_.bowtie2-mm9.log
bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2014_02_05_06_10_30_user_ION-32-PHLab_140205_ChIRP-seq_CPH1-4.CPH3.IonXpress_007.fastq |samtools view -Sb - > 007.bam 2> 007_.bowtie2-mm9.log
#bowtie2 --threads 8 --local --very-sensitive-local -x /data/results/reference/hg19/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/genome -U R_2014_02_05_06_10_30_user_ION-32-PHLab_140205_ChIRP-seq_CPH1-4.CPH4.IonXpress_008.fastq |samtools view -Sb - > 5.bam 2> 05_.bowtie2-mm9.log