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...
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 ...
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...
一旦你有了 FASTQ 文件和参考转录组,你就可以运行cellranger count了。 代码语言:javascript 复制 cellranger count--id=run_count_1kpbmcs \--fastqs=/mnt/f/Linux/run_cellranger_count/pbmc_1k_v3_fastqs \--sample=pbmc_1k_v3 \--transcriptome=/mnt/f/Linux/genomeAnno/hsa/refdata-gex-GRCh38-2020...
FastqToTagCountPluginData from: Next-generation sampling: pairing genomics with herbarium specimens provides species-level signal in Solidago (Asteraceae).Beck, James BSemple, John CBeck, J. B., Semple, J. C., 2015. Next-generation sampling: pairing genomics with herbarium specimens provides ...
_R1_*.fastq.gz | fastx_read_count stdin $ pigz -dc Sample_R1_*.fastq.gz | fastx_read_count stdin $ bzip2 -dc Sample_R1_*.fastq.bz2 | fastx_read_count stdin $ pbzip2 -dc Sample_R1_*.fastq.bz2 | fastx_read_count stdin $ xz -dc Sample_R1_*.fastq.xz | fastx_read_count ...
For experiments where only gene expression data is present, here are the arguments available for specifying which FASTQ filescellranger countshould use: ArgumentBrief Description --fastqs(Required) The folder containing the FASTQ files to be analyzed. Generally, this will be thefastq_pathfolder gener...
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 & ...
Generate a raw sgRNA read count table from fastq filesfqInfo