#!/bin/bash
#SBATCH --job-name=zBTmac-11
#SBATCH --output=zBTmac.11.out
#SBATCH --error=zBTmac.11.err
#SBATCH --time=24:00:00
#SBATCH -p akundaje,normal,owners,sfgf
#SBATCH --cpus-per-task=16
#SBATCH --mem=40000
python ~/code/PEFastqToTabDelimited.py /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-06-03-Symbiodinium-splicing/smic_nn_R2-SRR3337493_1.fastq.gz /oak/stanford/groups/akundaje/marinovg/Symbiodinium/2017-06-03-Symbiodinium-splicing/smic_nn_R2-SRR3337493_2.fastq.gz -trim 50 50 -trim5 10 10 | ~/programs/bowtie-1.0.1+hamrhein_nh_patch/bowtie ~/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.annotation -p 20 -e 200 -a --offrate 1 -t -X 1000 --sam --12 - | ~/programs/samtools-0.1.18/samtools view -bT ~/genomes/Dinoflagellata/Symbiodinium_microadriaticum_v1.0/bowtie-indexes/Smic.genome.annotation.fa - -o smic_nn_R2-SRR3337493.Smic.genome.annotation.a.e200.offrate1.bam