1.1 序列操作SeqKit提供了丰富的命令行选项，如 seqkit seq，让你轻松处理序列。例如，-p用于获取互补序列，--dna2rna转换DNA为RNA，-l转换为小写，-g移除组装序列中的间隙，-r反向序列，--rna2dna则用于RNA转DNA。你还可以控制每行输出的碱基数，如 seqkit seq ex.fasta -w 60，或者指定长度切...
-g, --remove-gaps 移除组装序列中的gap -r, --reverse 取反向序列 --rna2dna RNA to DNA -u, --upper-case 将序列以大写字母形式输出 -w, --line-width int 以每行指定长度输出序列 (0 for no wrap) (default 60) 举例: seqkit seq test.fa -w 0#将此文件fasta序列转换成一行输出 ...
root:~/refs# seqkit stat duplicated-reads.fq.gz 1.取序列名 seqkit fx2tab -n -i duplicated-reads.fq.gz | head 2.查看gc含量 seqkit fx2tab -n -i -g duplicated-reads.fq.gz | head 3.查看序列中任意碱基（或组合）的含量 seqkit fx2tab -n -i -B A -B T duplicated-reads.fq...
具体用法：通过添加环境变量调用，如`export PATH=path:$PATH`，并参照各种命令的参数选项进行操作，例如`seqkit seq -w 100 test.fa`以100碱基为行输出序列。例如，对文件进行长度统计和筛选特定序列：- seqkit fx2tab -l -g -n -i -H test.fa 显示序列长度和GC含量。- seqkit grep -s -p ...
# 选取有起始密码子的序列seqkitgrep-s-r-i-p^atg ex.fa# 根据ID提取序列seqkitgrep-flist ex.fa>new.fa# 简并碱基使用。S 代表C or G.seqkitgrep-s-d-i-pTTSAA# 匹配限定到某区域seqkitgrep-s-R1:30-i-r-pGCTGG# 2.5. motif定位 代码语言:shell ...
seqkit locate: Fix-G/--non-greedyfor tandem repeats, e.g., ATTCGATTCGATTCG (ATTCGx3). seqkit grep/subseq: Fix negative regions longer than sequence length.#479. seqkit stats: Add an extra columnsum_nto count the number of ambiguous characters.#490 ...
seqkit fq2fa: faster, and do not wrap sequences. seqkit grep/locate/mutate: detect unquoted comma and show warning message, e.g., -p 'A{2,}'. #250 SeqKit v2.0.0 - 2021-08-27 Performance improvements seqkit: faster FASTA/Q reading and writing, especially on FASTQ, see the ben...
12 A C G T N a c g t n -12:-1 A C G T N a c g t n Usage: seqkit split [flags] Flags: -i, --by-id split squences according to sequence ID -p, --by-part int split sequences into N parts -r, --by-region string split squences according to subsequence of given ...
⼀、序列操作 seqkit seq [flags] file 参数:-p, --complement 取互补序列 --dna2rna DNA to RNA -l, --lower-case 将序列以⼩写字母形式输出 -g, --remove-gaps 移除组装序列中的gap -r, --reverse 取反向序列 --rna2dna RNA to DNA -u, --upper-case 将序列以⼤写字母形式输出 -w, -...
seqkit sliding -g -s 40 -W 40 input.fasta -o out.fasta Attentions: Attention: 1. For the two-pass mode (-2/--two-pass), The flag -U/--update-faidx is recommended to ensure the .fai file matches the FASTA file. @@ -2791,7 +2791,7 @@ Usage ```text match up paired-end re...