单端测序(Single-read)和双端测序(Paired-end和Mate-pair)的关系,程序员大本营,技术文章内容聚合第一站。
Paired-end runs sequence both DNA ends, for easier analysis of rearrangements, novel transcripts, and more. Single-end runs offer an economical alternative.
FastQ 是大部分最原始scRNASeq的数据,所有的单细胞RNA-seq测序数据都是双端paired-end测序,barcode序列可能会出现在一个read或者两个reads内(依据使用protocol的不同),但是使用UMI的方法产生的数据,一个read会包含UMI/barcode/adapters但是由于测序长度原因会不包含转录本序列,所以这个方法后续的处理是以单端测序的形式处...
因为insert size是打断前的长度,打断之后便是reads,这里计算average reads长度。 shotgun sequencing鸟枪法:直接从生物细胞基因组中获取目的基因的方式 single-read :单端测序(200-500bp) Paired-end :双末端测序(200-500bp)因为双末端测序,所以中间被测序列称为insert,insert打断了之后的片段就是reads。 Mate-pair:...
Paired-end sequencing reads from the eight samples were preprocessed using 10× Genomics Cell Ranger 3.0 software for sample demultiplexing, barcode processing, and single-nucleus 3′ gene counting (single nuclei mode; counting performed on unspliced Ensembl transcripts, as described in the 10x Genomic...
Single-cell RNA sequencing analysis identified 12 B-cell subtypes and characterized the transcriptomic heterogeneity of B cells in muscle-invasive bladder cancer (MIBC). The interferon-stimulated B-cell subtype (B-ISG15) and germinal center-associated B-cell subtypes (B-LMO2, B-STMN1) were signi...
The tumor microenvironment (TME) in pancreatic ductal adenocarcinoma (PDAC) is a complex ecosystem that drives tumor progression; however, in-depth single cell characterization of the PDAC TME and its role in response to therapy is lacking. Here, we perform single-cell RNA sequencing on freshly ...
We developed a method to rigorously analyze L1 mRNA expression at a single-locus resolution by filtering out truncated and passively transcribed L1 sequences [12,20,30]. This method includes cytoplasmic RNA extraction, selection of polyadenylated transcripts, stranded paired-end sequencing, unique ali...
Here, we present a single-cell RNA sequencing atlas of immune cells from cartilaginous (white-spotted bamboo shark) and bony (zebrafish and Chinese tongue sole) fishes. Cross-species comparisons show that the same cell types across different species exhibit similar transcriptional profiles. In the ...
Exomes of 11 formalin-fixed and paraffin-embedded lung tumor tissues and paired blood samples were captured using the SureSelectXT Human All Exon V5 kit (5190-6208, Agilent, Santa Clara, CA, USA). Sequencing libraries were constructed for the HiSeq2500 system (Illumina, San Diego, CA, USA)...