trim_galore -q 20 --phred33 --stringency 3 --length 20 -e 0.1 --paired *64_1.fastq.gz *64_2.fastq.gz -o ../trimmed ls *_1.fastq.gz | sed 's/ _1.fastq.gz$//' | parallel -j 5 'trim_galore -q 20 --phred33 --length 20 -e 0.1 --paired --cores 2 -o ~/rna/test...
在该workflow中,所用的数据集来自RNA-seq,气道平滑肌细胞(airway smooth muscle cells )用氟美松(糖皮质激素,抗炎药)处理。例如,哮喘患者使用糖皮质激素来减少呼吸道炎症,在该实验设计中,4种细胞类型(airway smooth muscle cell lines )用1微米地塞米松处理18个小时。每一个cell lines都有对照与处理组(a treated ...
1.RNA-seq(4):Hisat2+FeatureCounts+DESeq2流程+作图! https://pzweuj.github.io/2018/07/18/rna-seq-4.html 2.一个植物转录组项目的实战 http://www.bio-info-trainee.com/2809.html 3.RNA_seq(1)植物转录组差异基因分析简单练习 https://www.jianshu.com/p/7146d5c41294 Part I II 基本是照着...
RNA sequencing (RNA-seq) is a crucial technique for many scientific studies and multiple models, and software packages have been developed for the processing and analysis of such data. Given the plethora of available tools, choosing the most appropriate ones is a time-consuming process that ...
RNA-Seq or miRNA data set — from bacteria to human— against a reference genome, and then offers extensive RNA-Seq data analysis tools to explore your results in-depth. Perform statistical analyses of differential gene expression using EdgeR or DESeq2, view Gene Set Enrichment Analysis (GSEA)...
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. - nf-core CI · Workflow runs · nf-core/rnaseq
Snakemake中的基本散装RNA-seq管线 目录 描述 该存储库包含两种基本形式的基本批量RNA-seq管道的演示,即Snakemake (在workflow/目录中)和bash脚本(在bash_workflow/目录中)。 这两个工作流程执行相同的分析,但是Snakemake管道更加健壮和推荐,尽管目前还不够完善。 这个Snakemake管道是作为教程的一部分而创建的,因此避免...
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. - nf-core branch protection · Workflow runs · nf-core/rnaseq
Background: With the cost of DNA sequencing decreasing, increasing amounts of RNA-Seq data are being generated giving novel insight into gene expression and regulation. Prior to analysis of gene expression, the RNA-Seq data has to be processed through a number of steps resulting in a quantifica...
General procedure for acquiring RNAseq raw data 4. Python analysis to get count-matrix of the RNAseq ### Quarlity control step $ fastqc -t 12 -o ./ your_rawdata_name_1.fq.gz your_rawdata_name_2.fq.gz ### Trimming for adaptors (Not required) ...