工具：seqtk?

head40.fq

a.list

從fasta/fastq文件中提取子集

????????????seqtk subseq head40.fq a.list

提取fq時(shí)需要其文件開頭用>:? sed -i 's/@/>@/g' head40.fq

工具：seqkit?

?????????? seqkit grep -f a.list head40.fq [輸出格式?jīng)]有樓上好]

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

提取補(bǔ)集：

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

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