WebHomer ChIP-seq analysis. Peak annotation with genomic features: TSS, intron, exon, etc. Find motifs; Motif scanning: Find which peaks contain the motif. Input motif is homer … WebChIP-eat combines both computational (high PWM score) and experimental (centrality to ChIP-seq peak summit) support to find high-confidence direct TF-DNA interactions in a ChIP-seq experiment-specific manner, uses the DAMO tool. Input data - ReMap 2024 and GTRD. Robust and permissive collections. Over 197,000 Cis-regulatory modules.
ChIP-seq Protocols And Methods - Springer Nature
WebThe following example generates the fingerprints for the invididual ENCODE histone mark ChIP-seq data sets and their corresponding input (focusing … WebWe have developed a footprinting method to predict TF footprints in active chromatin elements (TRACE) to improve the prediction of TFBS footprints. TRACE incorporates … cucumber nutrition facts without peel
plotFingerprint — deepTools 3.5.0 documentation
真核生物基因表达是一个复杂而有序的过程,它是众多反式作用因子和顺式作用元件之间相互作用的结果。反式作用因子是指能直接或间接识别和结合在顺式作用元件上,调控靶基因表达的蛋白质因子,一般也称为转录因子(transcriptional factor,TF),转录因子结合位点((Transcription factor binding site, TFBS)是与转录因 … See more 在本文开头提到的综述里有一个表,列出了目前所有可以进行footprinting分析的软件: 在这个表里的倒数第二列,标出了这些软件是否可以用来分 … See more 参考官网步骤:http://www.regulatory-genomics.org/rgt/rgt-data-folder/,这个软件支持的基因组文件有:hg19, hg38, mm9, mm10, zv9, … See more HINT还可以输出用于可视化peak的信号(比如IGV)。所以你还可以用下面的命令生成基因组配置文件(BigWig文件): 生成的bigwig文件包含ATAC-seq的read数量,这个数量是在信号 … See more NOTE:从这一步你需要注意的是,如果你用的是linux系统,你先需要保证上面提到的rgtdata这个文件夹放在home目录里。因为这个软件是高度依赖python的,我的conda是安装在 … See more WebChromatin immunoprecipitation, or ChIP, is an antibody-based technology used to selectively enrich specific DNA-binding proteins along with their DNA targets. ChIP is used to investigate a particular protein-DNA interaction, several protein-DNA interactions, or interactions across the whole genome or a subset of genes. WebMassachusetts Institute of Technology easter date of 2023