統(tǒng)計比對率
- 新建文件夾
mkdir flagstat
- 構建腳本前文件
ls *.bam > flagstat_bam
find *.bam>bam_sample
sed -i "s/.sort.bam/ /g" bam_sample
paste flagstat_bam bam_sample >flagstatbam_list
- 構建腳本
vim flagstatbam.sh
cat flagstatbam_list |while read id
do
arr=(${id})
bam=${arr[0]}
sample=${arr[1]}
samtools flagstat $bam > flagstat/$sample.flagstat.txt &
done
- 激活并運行腳本
chmod a+x flagstatbam.sh
nohup ./flagstatbam.sh
進入結果文件夾提取所需內容
cat * > flagstat
grep "0 mapped" flagstat > flagstats
cat flagstats | awk '{print $5}' > flag
sed -i "s/(/ /g" flag
sed -i "s/%/ /g" flag
cat flag
