Trim_galore

Trim_galore自动化过滤数据，十分适合小白，具体来说的话，trim_galore分几步处理数据：

1. Quality trimming;
2. Adaptor trimming;
3. Removing short sequences
4. Specialized trimming -hard- and epigenetic clock trimming

1. paired-end

mkdir $data/trimmed_data && cd $data/fastq
echo " trim_galore started at $(date)"
ls *gz |cut -d "_" -f 1-3 |sort -u |while read i; do R1=${i}_1.fq.gz; R2=${i}_2.fq.gz; trim_galore -q 25 --paired $R1 $R2 --phred33 --length 35 -e 0.1 --stringency 3 --gzip -o ../trimmed_data; done
## gzip: 将output进行压缩
echo "trim_galore finished at $(date)"

## length的话，36是最早ATAC的测序长度

2.single-end

ls $data/raw/*gz | while read i
do 
nohup trim_galore -q 25 --phred33 --length 25 -e 0.1 --stringency 4 -o $data/clean $i & 
done