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 ...
单个fastq(.gz)文件: ./FastqCount input.fastq 多文件: pigz-dcR1.fastq.gzR2.fastq.gz|./FastqCount->seq.out& 3. 结果
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...
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 ...
CSV全称Comma Separated Values是"逗号分隔值"的英文缩写.通常是纯文本文件,可以被文本编辑软件,Excel或...
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 & ...