fix BED coordinates for amplicons found in the minus strand.#367 seqkit split: fix forgetting to add extension for--two-pass.#332 seqkit stats: fix compute Q1 and Q3 of sequence length for one record.#353 seqkit grep: fix count number (-C) for matching with mismatch (-m > 0).#370 ...
#选取 key=feature value=gene的行 5.4 sequence 获取序列,从下文看,是根据下载的基因组文件和基因组注释文件,将对应部件的序列列出来,同时也可以提供序列开头和末尾的信息. get_tx_seq 获取fasta格式的transcript序列 gtftk get_tx_seq -g genome.fa -i SWO_genes.gtf less -SN # -g, --...
Hi, Background : I have some ONT data that I basecalled with Dorado and I wanted to process it with the Filtlong tool. The problem is that Filtlong does not allow duplicated read IDs and apparently, some were found in my data. I have sea...
(base)bio03@VM-0-6-ubuntu:~/opt/bin$ seqkit seqkit:command not found(base)bio03@VM-0-6-ubuntu:~/opt/bin$./seqkit # 使用./+软件名称可以调看详情和运行 SeqKit--a cross-platform and ultrafast toolkitforFASTA/Qfile manipulation Version:0.15.0Author:WeiShen<shenwei356@gmail.com>Documents:...
The version update to 2.9.0 matches the latest official release from November 1, 2024, which includes important fixes for sequence ID parsing and improvements to various SeqKit commands. 🧰 Tools 🪛 yamllint [error] 1-1: syntax error: found character '%' that cannot start any token ...
Sorting FASTA file in order of sequence size (small to large).$ seqkit sort --by-length viral.1.1.genomic.fna.gz > viral.1.1.genomic.sorted.fa If the files are too big, use flag --two-pass which consumes lesser memory.$ seqkit sort --by-length --two-pass viral.1.1.genomic.fna.gz...
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Describe your issue Seqkit locate does not seem to find fully overlapping patterns on the same strand (whether in greedy or non-greedy mode) For instance, the regex below for searching for ORFs, adapted from that provided, does not find ...
seqkit mutate: fix inserting sequence -i/--insertion, this bug occurs when insert site is big in some cases, don't worry if no error reported. seqkit replace: new flag -U/--keep-untouched: do not change anything when no value found for the key (only for sequence name). do no supp...