#!/bin/bash
# by YH
# Linux system, based on Cutadapt version 2.10
# 2022-07-08
# version 1
# After separate the mix-tso library, barcode information is uesed for separate the single-cell reads.
#

######################### After separate the mix 
currentline=1 ;
while read line;
do
cutadapt -j6 -g ^${line} -O5 -e0.1  --discard-untrimmed -o Test_N4_${line}.fastq.gz \
-p Test_N4_R1_${line}.fastq.gz \
Test_R2_N4.fastq.gz Test_R1_N4.fastq.gz;
((currentline=${currentline}+1)) ;
done<barcode.txt
