fastq-tools This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files. ...
seqkit translate -T 1 demo.fa-T参数指定使用的转换模式,1是一般模式。 提取上游2K的序列 seqkit subseq --up-stream 2000 -f --bed TM-1.bed TM-1.genome.fa 文件TM-1.bed格式是,染色体,start,end,geneid使用tab分割,TM-1.genome.fa是基因组文件 ...
--dont_overwrite don't overwrite existing files. Overwritting is allowed by default. --fix_mgi_id the MGI FASTQ ID format is not compatible with many BAM operation tools, enable this option to fix it. # adapter trimming options -A, --disable_adapter_trimming adapter trimming is enabled by...
Fastq文件得获取 ,可以从NCBI获取,也可以自己测序得到结果,下面介绍从网上获取数据。 linux 下安装SRA Toolkit工具 1、NCBI官网查看工具地址,并下载安装包 具体操作步骤如下: 打开NCBI官网 点击Download Tools并进入 找到SRA Toolskit 会转跳到github,复制下载连接,后续使用Linuxwget命令下载 打开Linux 总端,使用wget ...
Gordon A (2010) FASTX-Toolkit: FASTQ/A short-reads pre-processing tools. 1.0.0. The Hannon laboratory, Cold Spring Harbor laboratory. URL: http://hannonlab.cshl.edu/ fastx_toolkit/Gordon, A., and Hannon, G. 2010. FASTX-Toolkit: FASTQ/A short-reads preprocessing tools. http://hannonlab...
一、写在前面 fastp是一个基于C++用于处理fastq文件的一体化工具。其特点有: 1、功能多样:能够处理多种多样的过滤前/后fastq数据,能够检测质量曲线、碱基含量、...
2. 点击Submit进入数据提交页面,下拉至Other Tools 3. 选择GEO,点击Learn more,进入数据提交页面。 4.进入GEO数据提交页面后,点击“GEO”进入GEO主页(https://www.ncbi.nlm.nih.gov/geo/) GEO数据下载 1.输入数据集或者样本ID 2.进入GSE页面 需要确认此数据是否采用10X Genomics平台(summary可能包含单细胞测序平...
(http://maq.sourceforge.net/) And many many others. However, It is sometimes more productive to preprocess the FASTA/FASTQ files before mapping the sequences to the genome - manipulating the sequences to produce better mapping results. The FASTX-Toolkit tools perform some of these preprocessing...
生信软件8 - bedtools进行窗口划分、窗口GC含量、窗口测序深度和窗口SNP统计 生信软件9 - 多公共数据库...
conda create-c conda-forge-c bioconda-n kingfisher pigz python extern curl sra-tools pandas requests aria2 conda activate kingfisher #使用conda activate不能成功激活环境时可以尝试使用:source activate kingfisher pip install bird_tool_utils'>='0.2.17git clone https://github.com/wwood/kingfisher-downl...