计算测序深度

参考一
参考二

测序reads数两个例子

#singel end
folder_path="/path_to/donor2"
output_file="/path_to/donor2_nanopore_coverage_2.txt"

# 遍历文件夹中的所有fastq文件
for fastq_file in ${folder_path}/*.fastq; do
    # 使用SAMtools命令计算reads数量
    read_count=$(expr $(cat ${fastq_file} | wc -l) / 4)
    # 打印每个文件的reads数量
    echo "${fastq_file}: ${read_count} reads" >>$output_file
done

#pair end
folder_path="/path_to/short_reads/donor1"
output_file="/path_to/short_reads/donor1_short_reads_coverage.txt"

for i in 1 2 3 4 5 6 7 8
do
    read_count1=$(zcat "${folder_path}/s${i}_R1_val_1.fq.gz" | grep -c '^+$')
    read_count2=$(zcat "${folder_path}/s${i}_R2_val_2.fq.gz" | grep -c '^+$')
    read_count=$(expr($read_count1+$read_count2))
    echo "s${i}: ${read_count} reads" >>$output_file
done