bowtie-paired-genome-transcriptome,sh

#!/bin/bash
#$ -pe smp 8

in_fastq_1=$1; shift
in_fastq_2=$1; shift
out_sam=$1; shift
ref_virus=${1-/ifs/scratch/c2b2/rr_lab/avp2106/pathogen/refs/TYP1.fa}
ref_genome=/ifs/scratch/c2b2/rr_lab/shares/ref/hg19/bowtie2/genome/hg19
ref_transcriptome=/ifs/scratch/c2b2/rr_lab/shares/ref/hg19/bowtie2/transcriptome/transcriptome_fasta

#############################################
genome_suffix=genome_unmapped.fastq
mkfifo R1.$genome_suffix R2.$genome_suffix
/ifs/home/c2b2/rr_lab/shares/bin/bowtie2-2.0.2/bowtie2 -x $ref_genome -q \
    -1 $in_fastq_1 \
    -2 $in_fastq_2 \
    --un-conc R%.$genome_suffix \
    --local > /dev/null &

#############################################
transcriptome_suffix=transcriptome_unmapped.fastq
#mkfifo R1.$transcriptome_suffix R2.$transcriptome_suffix
/ifs/home/c2b2/rr_lab/shares/bin/bowtie2-2.0.2/bowtie2 -x $ref_transcriptome -q \
    -1 R1.$genome_suffix \
    -2 R2.$genome_suffix \
    --un-conc R%.$transcriptome_suffix \
    --local > /dev/null 

#############################################
# fqtrim_suffix=${transcriptome_suffix/fastq/fqtrim.fastq}
# mkfifo R1.$fqtrim_suffix R2.$fqtrim_suffix
# /ifs/scratch/c2b2/rr_lab/shares/fqtrim-0.92/fqtrim -p 2 -DV R1.$transcriptome_suffix,R2.$transcriptome_suffix -o fqtrim.fastq &

#############################################
# /ifs/home/c2b2/rr_lab/shares/bin/bowtie2-2.0.2/bowtie2 -p 2 -x $ref_virus -q \
#     -1 R1.$fqtrim_suffix \
#     -2 R2.$fqtrim_suffix \
#     --local \
#     | samtools view -SF4 - > $out_sam