Subcommand `rna`

Workflow `rna` usage

./scMaestro rna -h 
usage: scMaestro rna [-h] -f [FASTQPATH [FASTQPATH ...]] -g GENOME -r
                     REFERENCE FOLDER [--fullanalysis]
                     [--force FORCE | --expect EXPECT] [--exclude-introns]

optional arguments:
  -h, --help            show this help message and exit
  -f [FASTQPATH [FASTQPATH ...]], --fastqs [FASTQPATH [FASTQPATH ...]]
                        Path(s) to fastq files, multiple paths can be provided
                        together. eg. "-f path1 path2"
  -g GENOME, --genome GENOME
                        Genome build, e.g. "hg38", "mm10"
  -r REFERENCE FOLDER, --reference REFERENCE FOLDER
                        Reference folder for alignment. VDJ reference is
                        needed if subcommand "vdj" is used.
  --fullanalysis        Run full analysis pipeline
  --force FORCE         Run Cell Ranger with --force-cell
  --expect EXPECT       Run Cell Ranger with --expect-cells
  --exclude-introns     Exclude intronic reads in count. To maximize
                        sensitivity for whole transcriptome 3’/5’ Single Cell
                        Gene Expression and 3’ Cell Multiplexing experiments,
                        introns will be included in the analysis by default
                        for cellranger (>v7.0.0) count and multi.

Option '--fullanalysis'

If --fullanalysis is enabled. Quality control, PCA, clustering, annotation will be performed for each sample seperately using Seurat and SingleR. An html report will be generated. An example can be found here. You can donwload and visulaize the file in web browser.

Example data

Download the raw reads

wget https://s3-us-west-2.amazonaws.com/10x.files/samples/cell-exp/6.1.2/10k_PBMC_3p_nextgem_Chromium_X_intron/10k_PBMC_3p_nextgem_Chromium_X_intron_fastqs.tar
tar xvf 10k_PBMC_3p_nextgem_Chromium_X_intron_fastqs.tar
ls 10k_PBMC_3p_nextgem_Chromium_X_fastqs/ |cat 
10k_PBMC_3p_nextgem_Chromium_X_S1_L001_R1_001.fastq.gz
10k_PBMC_3p_nextgem_Chromium_X_S1_L001_R2_001.fastq.gz
10k_PBMC_3p_nextgem_Chromium_X_S1_L002_R1_001.fastq.gz
10k_PBMC_3p_nextgem_Chromium_X_S1_L002_R2_001.fastq.gz
10k_PBMC_3p_nextgem_Chromium_X_S1_L003_R1_001.fastq.gz
10k_PBMC_3p_nextgem_Chromium_X_S1_L003_R2_001.fastq.gz
10k_PBMC_3p_nextgem_Chromium_X_S1_L004_R1_001.fastq.gz
10k_PBMC_3p_nextgem_Chromium_X_S1_L004_R2_001.fastq.gz

Download the reference genome

Go to 10x Genomics website to download the pre-built reference. The link is here

Subcommand rna