根据seqid提取fastq序列

工具：seqtk 

head40.fq

a.list

从fasta/fastq文件中提取子集

            seqtk subseq head40.fq a.list

提取fq时需要其文件开头用>:  sed -i 's/@/>@/g' head40.fq

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工具：seqkit 

           seqkit grep -f a.list head40.fq [输出格式没有楼上好]

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samtools view WT-1.validpairs.bam | head

提取valid_seqid：

samtools view WT-1.validpairs.bam | awk '{print "@"$1}' | sort |uniq > WT-1.validpairs.seqid

提取原始fq_seqid:

zcat WT-1_R1.fq.gz | grep "@" | awk '{print $1}' | sort |uniq > WT-1.all.seqid

提取补集：

cat WT-1.all.seqid WT-1.validpairs.seqid WT-1.validpairs.seqid | sort | uniq -u > WT-1.discard.seqid

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直接grep：

提取validpairs：

for i in `head -n 10 WT-1.validpairs.seqid `

do 

echo "$i" grep validpairs ......

zcat ../02_rawfq/raw_fqgz_files/WT-1_R1.fq.gz | grep "$i"  -A 3 >>  WT-1.validpairs.R1.10.fq

zcat ../02_rawfq/raw_fqgz_files/WT-1_R2.fq.gz | grep "$i"  -A 3 >>  WT-1.validpairs.R2.10.fq

done

提取discard：

for i in `head -n 10 WT-1.discard.seqid `

do 

echo "$i" grep  discard ......

zcat ../02_rawfq/raw_fqgz_files/WT-1_R1.fq.gz | grep "$i"  -A 3 >> WT-1. discard.R1.10.fq

zcat ../02_rawfq/raw_fqgz_files/WT-1_R2.fq.gz | grep "$i"  -A 3 >>  WT-1. discard.R2.10.fq

done