做数据比较的时候,由于同一个样本测序数据量不一致,需要抽取数据,控制数据量基本一致。 自己写脚本速度较慢,后面发现一个不错的工具:seqtk 原始数据抽取 如果只控制原始数据量一致,过滤低质量数据后直接使用seqtk (Version: 1.3-r106) 的子模块seq, 配合参数 -s 设定随机种子,默认11; 配合参数 -f 设定抽取数据...
当请求坐标时,它们将以基于 1 的格式提供. gtftk nb_transcripts -i SWO_genes.gtf | gtftk select_by_key -k feature -v gene | gtftk tabulate -k gene_id,nb_tx -s "|" | less -SN 5.2 information 这部分的指令主要用于提取信息. count 计算特征的数量(转录本、基因、外显子...
zcat hairpin.fa.gz | seqkit grep -r -p ^hsa #提取ID开头为hsa的reads -v取想反zcat hairpin.fa.gz | seqkit grep -f list > new.fa #根据list取子集cat hairpin.fa.gz | seqkit grep -s -i -p aggcg #提取序列里有AGGCG的reads -m 允许误配的数量zcat hairpin.fa.gz | seqkit grep -s ...
7. grep序列 zcat hairpin.fa.gz | seqkit grep -r -p ^hsa #提取ID开头为hsa的reads -v取想反zcat hairpin.fa.gz | seqkit grep -f list > new.fa #根据list取子集cat hairpin.fa.gz | seqkit grep -s -i -p aggcg #提取序列里有AGGCG的reads -m 允许误配的数量zcat hairpin.fa.gz | seqk...
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. To install seqtk,git clone https://github.com/lh3/seqtk.git; cd seqtk; make...
注意,-s参数用于设定随机数种子,可以确保每次运行时选取的序列都是相同的。 5.将FASTQ文件转换为序列长度分布图: shell seqtk fqchk input.fastq > output.txt 这个命令将计算FASTQ文件中每个序列的长度,并生成一个分布图。 三、常见用例 Seqtk提供了许多实用的功能,适用于各种序列分析任务。下面是几个常见的用例:...
Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. To install seqtk,git clone https://github.com/lh3/seqtk.git; cd seqtk; make...
Where, input.fasta or input.fastq are the name of your input FASTA/FASTQ files, and ids.txt contains the list of sequences IDs (one ID per line) to extract from the FASTA/FASTQ files. The ids.txt can also contains the sequence ID and specific sequence regions, similar to three column...
Usage:seqtk sample[-2][-s seed=11]<in.fa><frac>|<number>#随机抽取序列,用法是seqtk sample fq/fa numOptions:-s INT RNG seed[11]#设置随机种子,默认11-22-passmode:twiceasslow butwithmuch reduced memory#占用更大的内存 $seqtk subseq ...
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