Cross-correlation plots课程中的示例数据Nanog_rep1的交叉相关图 ATAC-seq数据特有的fragment size分布 在第一篇ATAC-seq文章里面,如图: 可以使用atacQC 对 ATAC文库出 Fragment size distribution ,示例图如下: 参考资料 哈佛深度NGS数据分析课程https://github.com/hbctraining/In-depth-NGS-Data-Analysis-Course/tr...
ArchR主要以scATAC-seq原始数据经上游处理后的两种常见输出文件(BAM, fragment)作为输入。Fragment文件记录着scATAC-seq的fragment以及对应的细胞ID,每一行都是一条记录,该文件需要是tabix(见注1)排序并建立索引保证能被高效读取。BAM文件则是二进制格式下的tabix排序文件,记录着scATAC-seq的fragment、原始数据、细胞条...
ArchR主要以scATAC-seq原始数据经上游处理后的两种常见输出文件(BAM, fragment)作为输入。Fragment文件记录着scATAC-seq的fragment以及对应的细胞ID,每一行都是一条记录,该文件需要是tabix(见注1)排序并建立索引保证能被高效读取。BAM文件则是二进制格式下的tabix排序文件,记录着scATAC-seq的fragment、原始数据、细胞条...
ATAC-seq数据质量评估主要是看两个图,一个是插入片段分布图(Fragment Insertion Size Distribution),一个是TSS富集峰图。 插入片段分布图 ATAC-seq的插入片段分布有着非常鲜明的特点,一般把<100 bp的片段区域称NFR(Nucleosome-Free Region)也就是无核小体区,这部分区域也是转座酶最容易切割的区域,每隔10.5 bp就有...
Fragment size distribution TSS富集谱: 我们使用plotTSSEnrichment()函数绘制TSS富集谱。TSS富集谱需要在中心位置有一个明显的峰,在峰的右边还会有一个核小体引起的小隆起(约147 bp)。 p2<-plotTSSEnrichment(ArchRProj=projHeme1)p2 TSS enrichment profiles ...
Typical fragment size distribution plot shows enrichment around 100 and 200 bp, indicating nucleosome-free and mono-nucleosome-bound fragments. # ATAC-seq典型的片段长度分布,在100bp和200bp处会有峰,该峰分别是nucleosome-free与mono-nucleosome(核小体单体的)片段。 5.3Typical peak annotation 分布 Typical ...
做完比对后,我们仍然需要做质控,从unique mapping reads/rates,duplicated read percentages,fragment size distribution等等方面去评估。 如果遇到下面的情况,则reads需要被去除: 测序数据质量太差 PE测序中无法找到overlap区域 线粒体基因(因为线粒体基因都是可接近的,所以ATAC-seq数据中会有较多线粒体的序列,这部分需...
There are additional ATAC-seq-specific quality metrics that need to be evaluated. Typically, a successful ATAC-seq experiment should generate a fragment size distribution plot with decreasing and periodical peaks corresponding to the nucleosome-free regions (NFR) (< 100 bp) and mono-, di-, ...
An appropriate fragment size distribution is generally a prerequisite for a successful ATAC-seq assay. However, this metric alone is not necessarily a sufficient condition for a library to be of good quality. Thus, in our package, simple analysis of size distribution is integrated with several add...
Specific to ATAC-seq, an additional QC step is to check the fragment size distribution, which is expected to correspond to the length of nucleosomes:Assess fragment size distribution Remove mitochondrial readsATAC-seq experiments commonly include a high proportion of mitochondrial reads. These should ...