Step1. Bin barcode
./binReads.sh fastqFolder barcodes 1 8 16 p7.index p5.index usedBarcodes
where fastqFolder contains the fastq files and barcodes is the barcode index. 

Step2. Remove adaptor sequences

workingDir=/home/jz57w/mccb/Zhu/Guide-seq/ScotWolfe/rep1/binned/R2
cd $workingDir
for filename in *; do
   cutadapt -f fastq -b blue=TTGAGTTGTCATATGTTAATAACGGTAT -b red=ACATATGACAACTCAATTAAAC -b
 blueRevComp=ATACCGTTATTAACATATGACAACTCAA -b redRevComp=GTTTAATTGAGTTGTCATATGT -n 4 $filename >
 filtered_$filename
done
Step3. Map to the genome using bowtie2 and convert the alignment file to bed format with
CIGAR inforamtion

bowtie2 -p 16 --local --very-sensitive-local -x Bowtie2Index \
  -1 filtered_GUIDEseq_R1.fastq -2 filtered_GUIDEseq_R2.fastq \
  -S bowtie2.GUIDEseq.sam 

samtools view -bSq 30 bowtie2.GUIDEseq.sam  > bowtie2.${tag[${i}]}.bam
samtools sort bowtie2.GUIDEseq.bam bowtie2.GUIDEseq.sort
samtools index bowtie2.GUIDEsq.sort.bam
samtools sort -n bowtie2.GUIDEseq.bam bowtie2.GUIDEseq.sortname
bedtools bamtobed -cigar -i bowtie2.GUIDEseq.sortname.bam > bowtie2.${tag[${i}]}.sort.bed

Step4. Extract Umi sequence plus first 8 bases from the 5' end of the R1 read
./getUmi.sh testGetUmi 16 8