Total Sequences: 输入文本的reads的数量 Sequence length: 测序长度 %GC: GC含量,表示整体序列的GC含量,由于二代测序GC偏好性高,且深度越高,GC含量会越高。 (2)Per base sequence quality 横轴为read长度,纵轴为质量得分。 碱基质量值Q是每个碱基的正确识别率,是衡量测序质量的重要标准,Q-score = -10*lg(er...
# -a --adapters 也是输入一个文件,文件的格式Name [Tab] Sequence,储存的是测序的adpater序列信息,如果不输入,目前版本的FastQC就按照通用引物来评估序列时候有adapter的残留 # -q --quiet 安静运行模式,一般不选这个选项的时候,程序会实时报告运行的状况。
Benchmarking and new generative methods for single-cell transcriptome data in bulk RNA sequence deconvolution [https://www.researchsquare.com/article/rs-3338396/v1] BayesPrim 加载数据集 代码语言:javascript 复制 library("devtools")#install_github("Danko-Lab/BayesPrism/BayesPrism")# install.packages(...
E3/home/zhangyina/zbw_RNA-seq/stringtie/E3_count.gtf#将如上内容写入sample_lsit.txt,该文件为 \t(Tab) 分隔的两列,第一列为样本名称,第二列为定量的 GTF 文件的路径,注意最后不要有空行cat sample_lsit.txt#从https://github.com/gpertea/stringtie,下载prepDE.py3脚本python prepDE.py3-i sample_...
一般来说 RNA-Seq 重复率会比较高。ATCG 碱基占比容易出现前面碱基不稳定。多查看几个样本表现,如果波动模式差不多说明是随机引物不随机导致的,可以选择移除或不移除。 ATCG 占比前面碱基有波动 hisat2 比对 比对推荐 hisat2 不推荐 bowtie2. 因为 bowtie2 对剪切不友好,即使提高--maxins参数允许更长的片段...
10X genomics磁珠包裹在油滴里面,特点是磁珠上的探针组成:R1+barcode(name)+UMI(identify different RNA sequence)+poly。 Droplet特点是液滴中包裹细胞。 Single cell cDNA amplification即cDNA扩增三种方式: 1.PCR扩增 2.体外转录扩增 3.phi29聚合酶扩增PMA ...
受体库测序在传染病、过敏、自身免疫、肿瘤免疫和癌症免疫治疗研究中越来越广泛应用,但这是一种昂贵的检测方法,会消耗宝贵的组织样本。另一方面,RNA-seq数据包含组织或外周血单核细胞(PBMC)中表达的TCR和BCR序列。然而,由V(D)J重组和SHM产生的受体库序列与种系不同,因此在reads比对步骤中常常被剔除。
Single-cell RNA-seq analysis Database, preprocessing and integration We processed a total of 32,261 cells sourced from the GEO database under accession number GSE155788, which were originated from two CCM3WTmice (controls) and two CCM3KOmice (CCM model). Cell capture and library preparation we...
Single-cell RNA sequencingTumor microenvironmentDiagnosisPrognosisThe potential role of epithelium-specific genes through the adenoma-carcinoma sequence in the development of colorectal cancer (CRC) remains unknown. Therefore, we integrated single-cell RNA sequencing and bulk RNA sequencing data to select ...
Cost-efficient library generation by early barcoding has been central in propelling single-cell RNA sequencing. Here, we optimize and validate prime-seq, an early barcoding bulk RNA-seq method. We show that it performs equivalently to TruSeq, a standard