rsem-calculate-expression \--paired-end \ #双端测序--no-bam-output \ #不输出bam结果(bam是一种文件格式,sam->bam)--alignments-p16-q./04STAR_out/sampleAligned.toTranscriptome.out.bam \#比对所用的线程和输入文件./05rsem_index/Brapa_genome \#索引文件所在目录及其前缀./06rsem_out/sample_rsem...
STAR+RSEM 先比对再进行定量 # build index 建立索引; STAR --runThreadN 10 --runMode genomeGenerate \ --genomeDir arab_STAR_genome \ --genomeFastaFiles 00ref/TAIR10_Chr.all.fasta \ --sjdbGTFfile 00ref/Araport11_GFF3_genes_transposons.201606.gtf \ --sjdbOverhang 149 # 一般为read...
最常用的组合套装是STAR-RSEM和HISAT2-featureCounts以及HISAT2-HTSeq-count。从整体上看,RSEM很全面的,因为它调用了STAR做联配,所以效率高速度快,而且这个组合输出的文件相当丰富,除了基于基因组和转录本比对的bam文件,其定量文件还包含count、TPM、FPKM等,为后续分析提供很大便利。相比之下HISAT2-featureCounts的定...
Description of the bug When nextflow is started from an NFS mount (AWS EFS volume), the star_rsem aligner fails at the rsem-calculate-expression step. It appears that this step launches STAR and requires a file system supporting FIFO (na...
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. nf-co.re/rnaseq Resources Readme License MIT license Code of conduct Code of conduct Citation Cite this repository Activity Custom properties Stars 0 stars Watc...
RNA seq STAR与rsem的区别 目录 第一课 课程介绍 第二课 RNAseq技术 第三课 RNAseq发展历史 第四课 关于基因的概念 第一课 课程介绍 RNAseq捕获了细胞某一状态下所有的转录信息 DNA是静态信息、RNA是动态信息,是某一时刻DNA表达谱的快照 课程大纲
Subdivided starPathsRSEMT labelingA reverse edge magic total (REMT) labeling for the graph Γ = ( V (Γ), E (Γ)) along with cardinality of p = | V (G)| and q = | E (G)| respectively. A one-one map π : V (Γ) ∪ E (Γ) → {1, 2,,| V (Γ)|+| E (Γ)|} ...
FastQC Multiqc Trimmomatic STAR RSEM Subread HTSeq kallisto Deseq2 ...(conda可以安装) 查看软件是否可用,及时更新;准备好文件; ~/.bashrc screen-Shan #创建新窗口# 会话为dead状态。使用screen -wipe命令清除该会话# 鉴定是双端还是单端:计算fq.gz文件的reads;两个gz文件的reads数目相等,为双端测序;zcat-...
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. nf-co.re/rnaseq Topics workflow rna-seq pipeline nextflow rna nf-core Resources Readme License MIT license Code of conduct Code of conduct Citation Cite this repo...
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control. - yanqi219/rnaseq