Thecellranger count,cellranger vdj, andcellranger multipipelines are designed to process data from a single GEM well. To work with data from multiple GEM wells, you can aggregate and analyze the outputs from multiple runs of each of these pipelines usingcellranger aggr. ...
cellranger-atac reanalyze使用 cellranger-atac count 和 cellranger aggr 分析文件,使用可调参数设置重新运行二次分析 One sample, one GEM well, one flow cell One sample, one GEM well, multiple flow cells One sample, multiple GEM wells, one flow cell Multiple samples, multiple GEM wells, one flow...
在分析时,我们需要将混合的测序数据进行拆库demultiplex分成多个数据集,分别使用cellranger-atac count子程序进行独立分析,然后再使用cellranger-atac aggr子程序进行整合分析。 image.png Multiple Samples, Multiple GEM Wells, One Flowcell 在该分析流程中,我们对多个样本进行测序,每个样本分别使用不同的GEM wells进行...
When doing large studies involving multiple biological samples (or multiple libraries / replicates of the same sample), it is best to runcellranger counton each of the libraries individually, and then pool the results usingcellranger aggr. Thecellranger aggrcommand takes a CSV file specifying a ...
Learn more about when to use multiple CMOs per sample here. [gene-expression] reference,/path/to/transcriptome [libraries] fastq_id,fastqs,feature_types gex1,/path/to/fastqs,Gene Expression mux1,/path/to/fastqs,Multiplexing Capture [samples] sample_id,cmo_ids sample1,CMO301|CMO302 sample2...
Choosing a pipeline Library types GEX + Antibody/CRISPR (count) VDJ-T/B only (vdj) 3'/5' Sample Multiplexing (multi) VDJ + GEX + Antibody/CRISPR/BEAM (multi) Flex (multi) Secondary Analysis Aggregate Multiple Samples (aggr) Cell Annotation (annotate) Custom Analysis (reanalyze) Outputs...
Caused by: Process `NFCORE_SCRNASEQ:SCRNASEQ:CELLRANGER_ALIGN:CELLRANGER_COUNT` input file name collision -- There are multiple input files for each of the following file names: Sample_Y/S10_L001_R1_001.fastq.gz, Sample_Y/S10_L001_R2_001.fastq.gz So maybe we will have to work on ...
这里面的sample_feature_bc_matrix与cell ranger count得到的filtered_feature_bc_matrix类似 4.将count文件中的bam文件转变为loom(为了方便scVelo计算RNA速率) 因为cellranger multi的结果文件格式和cellranger count的结果文件格式不全相同,所以更推荐使用velocyto run而非velocyto run10x ...
cellcount aggr(一般不需要做) Many experiments involve generating data for multiple samples that are processed through different [Gel Bead-in Emulsion (GEM) wells] on Chromium instruments. Depending on the experimental design, these could be replicates from the same set of cells, cells from differen...
cellranger aggraggregates outputs from multiple runs ofcellranger countorcellranger multi, normalizing those runs to the same sequencing depth and then recomputing the feature-barcode matrices and analysis on the combined data. Theaggrpipeline can be used to combine data from multiple samples int...