Convert unmapped BAM files to FASTQ and remove adapters for single-end experiments

bam2fastq_trim_SE.sh

#!/bin/bash

cutadapt=`which cutadapt`
fastqc=`which fastqc`
bam2fastq=`which bam2fastq`
gzip=`which gzip`
origdir="."
results="cutadapt"
fastqcdir="${results}/FastQC"
adapter5="AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT"
a3="CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCAGACGTGTGCTCTTCCGATC"
indexC1_R1="TGGTCA" # TGACCA
indexC1_R2="CTGATC" # GATCAG
indexC2_R1="ATTGGC" # GCCAAT
indexC2_R2="AAGCTA" # TAGCTT
indexC3_R1="GATCTG" # CAGATC
indexC3_R2="GTAGCC" # GGCTAC
indexC4_R1="TCAAGT" # ACTTGA
indexC4_R2="TACAAG" # CTTGTA
inprefix="C"
outprefix="D"
samples=4
froms=1
replicates=2
threads=30

if ! [ -d "$results" ]; then
        mkdir -p $results
fi

if ! [ -d "$fastqcdir" ]; then
        mkdir -p $fastqcdir
fi

for s in $(seq $froms $samples)
do
	for r in $(seq 1 $replicates)
	do
		sample=${inprefix}${s}_R${r}
		outsample=${outprefix}${s}_R${r}
		if [ $sample == "C1_R1" ]; then
			adapter3index=${indexC1_R1}
		elif [ $sample == "C1_R2" ]; then
			adapter3index=${indexC1_R2}
		elif [ $sample == "C2_R1" ]; then
			adapter3index=${indexC2_R1}
		elif [ $sample == "C2_R2" ]; then
			adapter3index=${indexC2_R2}
		elif [ $sample == "C3_R1" ]; then
			adapter3index=${indexC3_R1}
		elif [ $sample == "C3_R2" ]; then
			adapter3index=${indexC3_R2}
		elif [ $sample == "C4_R1" ]; then
			adapter3index=${indexC4_R1}
		elif [ $sample == "C4_R2" ]; then
			adapter3index=${indexC4_R2}
		else
			echo "Could not assign 3' index adapter, exiting..."
			exit 555	
		fi 	
		adapter3="${adapter3index}${a3}"
		echo "processing $sample"
		echo "5' adapter: ${adapter5}"
		echo "3' adapter: ${adapter3}"
		rd="${origdir}/${sample}.fastq"
		outrd="${results}/${outsample}.fastq"
	
		# process original BAM file; convert to FASTQ and do QC	
		$bam2fastq -q ${sample}.bam -o $rd
		$fastqc --quiet --noextract -o $fastqcdir -t $threads $rd && $gzip -c $rd > ${origdir}/${sample}.fq.gz &
		# end procesing original files
	
		echo "cutadapt infile: $rd"
		echo "cutadapt outfile: $outrd"
		if ! [ -f "$rd" ]; then
			echo "ERROR: $rd not available"
		fi
		
		set -x
		# run cutadapt in single-end mode && rm non-clipped FASTQ file && run FastQC
		$cutadapt -q 30 -m 25 -g $adapter5 -a $adapter3 -o $outrd $rd  1> cutadapt_${sample}.out 2> cutadapt_${sample}.err && rm $rd && $fastqc --quiet --noextract -o $fastqcdir -t $threads $outrd && $gzip $outrd & 
		set +x
	done
done