Output descriptions

Here’s the output directory structure: each line represents a file or folder, indicated by “├──”, and the numbers indicate three important output files.

.
├── PBMC_report.html
├── PBMC_summary.csv
├── PBMC_summary.json
├── step1
│   ├── PBMC_1.fq.gz
│   ├── PBMC_2.fq.gz
│   ├── PBMC_multi_1.fq.gz
│   ├── PBMC_multi_2.fq.gz
│   └── PBMC_multi.json
├── step2
│   ├── featureCounts
│   │   ├── counts.txt
│   │   ├── counts.txt.summary
│   │   └── PBMC_SortedByName.bam
│   └── STAR
│       ├── downbam
│       │   ├── log.txt
│       │   ├── PBMC.bed
│       │   ├── PBMC.down.0.1.bam
│       │   ├── PBMC.down.0.1.bam.bai
│       │   ├── PBMC.geneBodyCoverage.curves.pdf
│       │   ├── PBMC.geneBodyCoverage.r
│       │   ├── PBMC.geneBodyCoverage.txt
│       │   └── PBMC.reduction.bed
│       ├── PBMC_Log.final.out
│       ├── PBMC_Log.out
│       ├── PBMC_Log.progress.out
│       ├── PBMC_SJ.out.tab
│       ├── PBMC_SortedByCoordinate.bam
│       ├── PBMC_SortedByCoordinate.bam.bai
│       ├── PBMC_SortedByName.bam
│       ├── PBMC__STARtmp
│       ├── report.pdf
│       ├── rnaseq_qc_results.txt
│       └── rRNA
│           ├── counts.txt
│           ├── counts.txt.summary
│           ├── PBMC_Aligned.out.bam
│           ├── PBMC_Aligned.out.bam.featureCounts.bam
│           ├── PBMC_Log.final.out
│           ├── PBMC_Log.out
│           ├── PBMC_Log.progress.out
│           ├── PBMC_SJ.out.tab
│           ├── PBMC__STARtmp
│           └── PBMC.xls
├── step3
│   ├── counts.xls
│   ├── detail.xls
│   ├── filtered_feature_bc_matrix
│   │   ├── barcodes.tsv.gz
│   │   ├── features.tsv.gz
│   │   └── matrix.mtx.gz
│   ├── raw_feature_bc_matrix
│   │   ├── barcodes.tsv.gz
│   │   ├── features.tsv.gz
│   │   └── matrix.mtx.gz
│   └── umi.xls
└── step4
    ├── biotype_FindAllMarkers.xls
    ├── FeatureScatter.png
    ├── FindAllMarkers.xls
    ├── lncgene_FindAllMarkers.xls
    ├── mito_quantile.xls
    ├── nCount_quantile.xls
    ├── nFeature_quantile.xls
    ├── PBMC.rds
    ├── resolution.xls
    ├── top10_heatmap.png
    ├── tsne.png
    ├── tsne_umi.png
    ├── tsne_umi.xls
    ├── umap.png
    └── VlnPlot.png

1. The file “PBMC_report.html” is a sample HTML report of the sample.

2. The file “PBMC_summary.csv” contains quality control information of the sample in CSV format.

3. The file “step3/filtered_feature_bc_matrix” is the filtered expression matrix after applying filtering steps.

4. The file “step4/PBMC.rds” is an RDS file containing the matrix that has been processed using Seurat.