#!/bin/bash
#$ -cwd -V

module load EBModules-LegacyBNB GCC/7.3.0-2.30 OpenMPI/3.1.1 Bowtie2/2.3.4.2

bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_P2F3_H3K27ac_S2_R1_001.fastq.gz -2 20250213_SW982_CR_P2F3_H3K27ac_S2_R2_001.fastq.gz -S P_H3K27ac_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_P2F3_HA_S4_R1_001.fastq.gz -2 20250213_SW982_CR_P2F3_HA_S4_R2_001.fastq.gz -S P_HA_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_P2F3_IgG_S1_R1_001.fastq.gz -2 20250213_SW982_CR_P2F3_IgG_S1_R2_001.fastq.gz -S P_IgG_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_P2F3_POU2F3_S3_R1_001.fastq.gz -2 20250213_SW982_CR_P2F3_POU2F3_S3_R2_001.fastq.gz -S P_P2F3_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T1P2F3_H3K27ac_S6_R1_001.fastq.gz -2 20250213_SW982_CR_T1P2F3_H3K27ac_S6_R2_001.fastq.gz -S T1P_H3K27ac_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T1P2F3_HA_S8_R1_001.fastq.gz -2 20250213_SW982_CR_T1P2F3_HA_S8_R2_001.fastq.gz -S T1P_HA_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T1P2F3_IgG_S5_R1_001.fastq.gz -2 20250213_SW982_CR_T1P2F3_IgG_S5_R2_001.fastq.gz -S T1P_IgG_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T1P2F3_POU2F3_S7_R1_001.fastq.gz-2 20250213_SW982_CR_T1P2F3_POU2F3_S7_R2_001.fastq.gz -S T1P_P2F3_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T1P2F3_POU2F3_S7_R1_001.fastq.gz-2 20250213_SW982_CR_T1P2F3_POU2F3_S7_R2_001.fastq.gz -S T1P_P2F3_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T2P2F3_H3K27ac_S10_R1_001.fastq.gz -2 20250213_SW982_CR_T2P2F3_H3K27ac_S10_R2_001.fastq.gz -S T2P_H3K27ac_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T2P2F3_HA_S12_R1_001.fastq.gz -2 20250213_SW982_CR_T2P2F3_HA_S12_R2_001.fastq.gz -S T2P_HA_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T2P2F3_IgG_S9_R1_001.fastq.gz -2 20250213_SW982_CR_T2P2F3_IgG_S9_R2_001.fastq.gz -S T2P_IgG_hg38.sam
bowtie2 -p 16 -x /grid/vakoc/data/oeldemer/hg38_genome/hg38_genome -1 20250213_SW982_CR_T2P2F3_POU2F3_S11_R1_001.fastq.gz -2 20250213_SW982_CR_T2P2F3_POU2F3_S11_R2_001.fastq.gz -S T2P_P2F3_hg38.sam