A decade ago, the first bioinformatics pipelines to detect circular RNA molecules based on short-read sequencing data were published. Here, we show that dozens of such circular RNA detection tools differ vastly in their sensitivity but not in their specificity. Analysis | 13 July 2023 Large-sca...
Once reads are obtained from well-designed scRNA-seq experiments, quality control (QC) is performed. Of the existing QC tools available, FastQC (Babraham Institute,http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) is a popular tool for inspecting quality distributions across entire reads....
# 首先我们切换到输出目录 cd /public/home/rnaseq # 这个 alias 命令很重要,因为官方的 pipeline 里找不到 hisat2_extract_splice_sites.py 这个文件在哪,所以你要告诉它在哪里 ## hisat2_extract_splice_sites.py 这个文件就是 hisat2 软件自带的,大家去官网搜索下载就行。 alias hisat2_extract_splice...
https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ STAR-counts的计算比较直截了当,就是有几条reads比对到相应的基因上面,counts就是几。 TPM,FPKM和FPKM_UQ的定义如下。 代码语言:javascript 代码运行次数:0 运行 AI代码解释 FPKMThe fragments per kilobaseoftranscript per milli...
为了便于在用户创建的管道中使用协调数据,可以在GDC数据门户中的几个中间步骤中访问RNA-Seq基因表达。以下是可在GDC Data Portal中下载的每种文件类型的说明。 参开资料: 1.https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/ ...
nf-core/rnafusionis a bioinformatics best-practice analysis pipeline for RNA sequencing consisting of several tools designed for detecting and visualizing fusion genes. Results from up to 5 fusion callers tools are created, and are also aggregated, most notably in a pdf visualiation document, a ...
limited. Some commercial companies provide software tools, such as 10× Genomics and Fluidigm, but this area remains in its infancy, and gold-standard tools have yet to be developed. In the sections below, we will discuss current bioinformatics tools available for the analysis of scRNA-seq data...
foriin`seq 48 62`;doprefetchSRR35899${i}done 还可以多个一起下载 先找到要下载的页面,比如https://www.ncbi.nlm.nih.gov/sra,然后右上角,send to-file,format选择accession list,保存为一个file(默认是SraAccList.txt),然后prefetch $(<SraAccList.txt) ...
nf-core/rnaseqis a bioinformatics pipeline that can be used to analyse RNA sequencing data obtained from organisms with a reference genome and annotation. It takes a samplesheet and FASTQ files as input, performs quality control (QC), trimming and (pseudo-)alignment, and produces a gene expres...
RNA-seq and bioinformatics were used to investigate the molecular mechanism of ZNF580 activity. ZNF580 inhibited neuronal death via interacting with the genes Krüppel-like factor 9 (KLF9), insulin-like growth factor-binding protein 3 (IGFBP3), heat shock protein family A (Hsp70) member 5 (...