cellranger使用

0. cellranger

cellranger -h
cellranger cellranger-6.1.2
Process 10x Genomics Gene Expression, Feature Barcode, and Immune Profiling data

USAGE:
    cellranger <SUBCOMMAND>

FLAGS:
    -h, --help       Prints help information
    -V, --version    Prints version information

SUBCOMMANDS:
    count               Count gene expression (targeted or whole-transcriptome) and/or feature barcode reads from a single sample and GEM well
    multi               Analyze multiplexed data or combined gene expression/immune profiling/feature barcode data
    vdj                 Assembles single-cell VDJ receptor sequences from 10x Immune Profiling libraries
    aggr                Aggregate data from multiple Cell Ranger runs
    reanalyze           Re-run secondary analysis (dimensionality reduction, clustering, etc)
    targeted-compare    Analyze targeted enrichment performance by comparing a targeted sample to its cognate parent WTA sample (used as input for targeted gene
                        expression)
    targeted-depth      Estimate targeted read depth values (mean reads per cell) for a specified input parent WTA sample and a target panel CSV file
    mkvdjref            Prepare a reference for use with CellRanger VDJ
    mkfastq             Run Illumina demultiplexer on sample sheets that contain 10x-specific sample index sets
    testrun             Execute the 'count' pipeline on a small test dataset
    mat2csv             Convert a gene count matrix to CSV format
    mkref               Prepare a reference for use with 10x analysis software. Requires a GTF and FASTA
    mkgtf               Filter a GTF file by attribute prior to creating a 10x reference
    upload              Upload analysis logs to 10x Genomics support
    sitecheck           Collect linux system configuration information
    help                Prints this message or the help of the given subcommand(s)

1. cellranger mkfastq

在这里插入代码片

2. cellranger count

返回的文件及其含义

.outs
├── analysis【数据分析文件夹】
│   ├── clustering【聚类，图聚类和k-means聚类】
│   ├── diffexp【差异分析】
│   ├── pca【主成分分析线性降维】
│   └── tsne【非线性降维信息】
├── cloupe.cloupe【Loupe Cell Browser 输入文件】
├── filtered_feature_bc_matrix【很重要，Seurat, Monocle的输入文件】
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├── filtered_feature_bc_matrix.h5【过滤掉的barcode信息HDF5 format】
├── metrics_summary.csv【CSV format数据摘要】
├── molecule_info.h5【aggregate的时候会用到的文件】
├── raw_feature_bc_matrix【原始barcode信息】
│   ├── barcodes.tsv.gz
│   ├── features.tsv.gz
│   └── matrix.mtx.gz
├──  possorted_genome_bam.bam【比对文件】
├──  possorted_genome_bam.bam.bai【索引文件】
├── raw_feature_bc_matrix.h5【原始barcode信息HDF5 format】
├── web_summary.html【网页简版报告以及可视化】
└── *_gene_bar.csv_temp【过程文件】