StringTie2是一种用于基因组上的转录组组装和定量的软件工具,其定量原理基于RNA-seq数据的读数。 在转录组组装过程中,StringTie2首先将原始的RNA-seq读取映射到参考基因组上,以确定每个转录本的外显子区域和边界。通过将转录本的外显子信息与基因组注释文件进行比较,可以对转录本进行分类,以确定它们是否属于已知的基因...
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wget http://ccb.jhu.edu/software/stringtie/dl/gffcompare-0.11.5.Linux_x86_64.tar.gz tar-zxvf gffcompare-0.11.5.tar.gz echo'export PATH=~/RNA-Seqruanjian/gffcompare-0.11.5.Linux_x86_64:$PATH'>>~/.bashrc 5、Deseq2和clusterProfiler Deseq2:基因差异表达分析的工具,能利用RNA-Seq实验的数据,...
StringTie2 tries to assemble reads. Put another way, FLAIR focuses on reconstructing full-length isoforms, while StringTie2 reconstructs isoforms based on potential splice sites identified from the reads. In this analysis, we found out that FLAIR might be better at identifying annotated ...
git clone https://github.com/mpertea/stringtie2 cd stringtie2 make release Note that simply runningmakewill produce an executable which is more suitable for debugging and runtime checking but which can be significantly slower than the optimized version which is obtained by usingmake release. ...
In order to build StringTie from this GitHub repository the following steps can be taken: git clone https://github.com/mpertea/stringtie2 cd stringtie2 make release Note that simply running make will produce an executable which is more suitable for debugging and runtime checking but which can...
RNA sequencing using the latest single-molecule sequencing instruments produces reads that are thousands of nucleotides long. The ability to assemble these long reads can greatly improve the sensitivity of long-read analyses. Here we present StringTie2,
样本定量软件stringtie 差异表达分析R语言包deseq2 package或ballgown package 以下代码以单个样本为例: 1. 测序结果Raw data的分析 #生成文件的md5值 md5sum *.gz > md5.txt #比对md5值 md5sum -c md5.txt #fastqc查看样本质量 fastqc -t 6 *gz -o result/ ...
id=${id/.sam/} samtools view -bS ${id}.sam -o /disk/zhanglu/SE8/bam/${id}.bam done -b 输出bam文件 -S 输入sam文件 samtools sort排序 #!/bin/bash #this is a sort ls *.bam | while read id do id=${id/.bam/} samtools sort ${id}.bam -T tmp -o ${id}.sort.bam ...
stringtie -p 10 -G Mus_musculus.GRCm38.102.gtf -l test1 -o test1.gtf test1.sorted.bam5. 注释文件合并# 创建 mergelist.txt 文件,指明组装后注释文件的路径 path/to/test1.gtf path/to/test2.gtf path/to/test3.gtf # 合并gtf文件 $ stringtie --merge -p 10 -G ./Mus_musculus.GRCm...