原始数据质控

软件：fastqc,multiqc

先使用fastqc将多个样本逐个进行质控，再使用multiqc将所有的样本质控结果合并汇总，方便查看比较每个样本的测序数据情况。

FastQC

```

#!/usr/bin/bash

start=$(date +%s)

echo "start time: $start";

echo $HOSTNAME

for i in *.fastq.gz; do fastqc -o $out_dir $i;done

end=$(date +%s)

echo "end time: $end";

runtime_s=$(echo $(( end - start )))

echo "Total run time(s): $runtime_s";

sec_per_min=60

sec_per_hr=3600

runtime_m=$(echo "scale=2; $runtime_s / $sec_per_min;" |bc)

echo "total run time(m): $runtime_m";

runtime_h=$(echo "scale=2;$runtime_s / $run_per_hr;" |bc)

echo "total run time(h) : $runtime_h";

```

MultiQC

```

multiqc -o $out_dir $in_dir

```

去除测序接头和低质量碱基,再重复一遍质控步骤

trim_galore

```

trim_galore --gzip --phred33 --illumina --output_dir $out_dir --paired ${sample}_R1.raw.fq.gz ${sample}_R2.raw.fq.gz

```