FastqCount(https://github.com/zhimenggan/FastqCount)主要用来计算fastq文件的reads数量、base数、Q20和Q30等指标,同时需要配合pigz一起来使用。 1.软件安装 安装pigz conda install pigz 安装FastqCount #从github下载FastqCount wget https://github.com/zhimenggan/FastqCount/archive/refs/heads/master.zip chmod ...
https://github.com/zhimenggan/FastqCount 统计指标包括: Total Reads Total Bases N Bases Q20 Q30 GC 2. 使用 压缩文件可搭配pigz使用更香。 单个fastq(.gz)文件: ./FastqCount input.fastq 1. 多文件: pigz -dc R1.fastq.gz R2.fastq.gz | ./FastqCount - >seq.out & 1. 3...
1. FastqCount简介 快速实用小工具:FastqCount https://github.com/zhimenggan/FastqCount 统计指标包括: Total Reads Total Bases N Bases Q20 Q30 GC 2. 使用 压缩文件可搭配pigz使用更香。 单个fastq(.gz)文件: ./FastqCount input.fastq 多文件: pigz-dcR1.fastq.gzR2.fastq.gz|./FastqCount->seq.out...
Tiny program to count reads in FASTA/FASTQ files. Contribute to agordon/fastx_read_count development by creating an account on GitHub.
An easy to use python-based package for generating ASAPseq Count Matrices from FASTQ files Quick Start The countASAP package can be installed either by downloading this repository and running the scripts in the countASAP directory, or by installing the script directly to your command line using:...
https://github.com/zhimenggan/FastqCount 统计指标包括: Total Reads Total Bases N Bases Q20 Q30 GC 2. 使用 压缩文件可搭配pigz使用更香。 单个fastq(.gz)文件: ./FastqCount input.fastq 1. 多文件: pigz -dc R1.fastq.gz R2.fastq.gz | ./FastqCount - >seq.out & ...
gitclonehttps://github.com/zhimenggan/FastqCount.gitchmod a+x FastqCount_v0.5 使用FastqCount统计fastq文件基本信息 cd/public/jychu/microRNA-goose~/soft/FastqCount/FastqCount_v0.5V0-1_L1_I302.R1.fastq.gz 结果如下 image https://www.jianshu.com/p/ad3265a2be09...
alevin比对率45%左右,这一点在Alevin github issue中有人提问过,开发者给出的回答是:STAR(或Hisat2)给出的比对率是全基因组的比对率,比对上的reads不一定是转录本,而alevin的比对率是reads比对至基因组转录本的比率。 差异可能来自于: 转录本的比对和技术策略:比对和“假比对”的技术差异 ...
This is a simple tool to calculate reads number and total base count in FASTQ file. Modified from http://lh3lh3.users.sourceforge.net/parsefastq.shtml. Compile: gcc -o kseq_fastq_base kseq_fastq_base.c -lz Usage: kseq_fastq_base [input.fq] FASTQ files could be gzipped! ^_^. The ...