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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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. ...
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 ...
用在64-bit ARMv8 上stringtie_2.2.1+ds-2_arm64.deb的下載頁面 如果您正在使用 Ubuntu,請儘量使用像aptitude或者synaptic 的套件管理程式,代替人工手動操作的方式從這個網頁下載並安裝套件。 您可以使用以下列表中的任何一個鏡像站,只要在您的/etc/apt/sources.list文件中像下面這樣添加一行: ...
一、安装软件 1、HISAT2 将reads比对到基因组上 2、StringTie 将比对好的reads进行拼装并预计表达水平 3、SAM tools 课上已经用sudo a...
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,
skovaka / stringtie2 Public forked from mpertea/stringtie2-initial-release Notifications Fork 1 Star 9 Code Pull requests Actions Projects Security Insights CommitsBranch selector master User selector All users DatepickerAll time Commit History Commits on Jun 3, 2019 restore SuperReads_...
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/ ...