### Run installation test

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/tutorials/setup-spaceranger

Verifies the installation by running a test pipeline, with or without internet access.

```bash
# With internet access
spaceranger testrun --id=verify_install

# Without internet access
spaceranger testrun --no-internet --id=verify_install

# Expected output
Martian Runtime - v4.0.5

Running preflight checks (please wait)...
Checking sample info...
Checking FASTQ folder...
Checking reference...
Checking reference_path
Checking optional arguments...

...

Pipestance completed successfully!
```

--------------------------------

### Uncompress Example Dataset

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/fastqs-demultiplexing-with-illumina-software

Uncompress the downloaded dual-indexed iSeq example dataset using the tar command. This prepares the data for running BCL Convert.

```bash
tar -xf /working-directory/iseq-DI.tar.gz

```

--------------------------------

### BCL Convert Execution Log Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/fastqs-demultiplexing-with-illumina-software

View an example of the console output after a successful BCL Convert run, including version information, command line used, and conversion completion status.

```text
bcl-convert Version 00.000.000.4.00.5
Copyright (c) 2014-2018 Illumina, Inc.
Command Line: --bcl-input-directory iseq-DI --output-directory tiny-FASTQs --sample-sheet bcl_convert_samplesheet.csv
# CPU hw threads available: 48
Parallel Tiles: 1. Threads Per Tile: 48
SW compressors: 48
SW decompressors: 24
Conversion Complete.

```

--------------------------------

### 10x Cloud Model CSV Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/space-ranger-annotate-outputs

Example content for a 10x Cloud model CSV file, including cell count support metrics for annotations.

```csv
barcode,coarse_cell_type,fine_cell_type,cell_count_in_model,coarse_cell_type_unfiltered,umi_count
cellid_000000054-1,epithelial cell,luminal cell of prostate epithelium,500,epithelial cell,1094
cellid_000000055-1,epithelial cell,luminal cell of prostate epithelium,488,epithelial cell,788
cellid_000000057-1,epithelial cell,luminal cell of prostate epithelium,486,epithelial cell,1084
```

--------------------------------

### Create and Navigate to Working Directory

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/tutorials/setup-spaceranger

Use these commands to create a dedicated directory for the Space Ranger tutorial and change into it. This helps organize your installation.

```bash
# Create working directory
mkdir spaceranger_tutorial

# Change directory
cd spaceranger_tutorial

```

--------------------------------

### View Pipestance Log

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/sr-troubleshooting

Examine the `_log` file in the output directory to view the parameters used to start an existing pipestance.

```bash
head -n20 /home/jdoe/runs/sample345/_log
```

--------------------------------

### PCA Components Matrix Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/secondary-analysis-csv

An example of the `components.csv` file header and first data row. It shows the Principal Component (PC) and the loadings for various Ensembl IDs (features).

```csv
PC,ENSG00000228327,ENSG00000237491,ENSG00000177757,ENSG00000225880,...,ENSG00000160310
1,-0.0044,0.0039,-0.0024,-0.0016,...,-0.0104
```

--------------------------------

### PCA Variance Explained Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/secondary-analysis-csv

An example of the `variance.csv` file content, showing each Principal Component (PC) and the proportion of variance it explains.

```csv
PC,Proportion.Variance.Explained
1,0.006020454455283148
2,0.0014744138318528535
3,0.0012400447266735174
4,0.0009462466452900335
5,0.0009012382233475119
6,0.0008795663315577918
7,0.0008772635528060896
8,0.0008770449415125795
9,0.0008671600964701859
10,0.0008598483035027898
```

--------------------------------

### Verify Space Ranger Installation

Source: https://www.10xgenomics.com/support/software/space-ranger/downloads/space-ranger-installation

Run the `spaceranger testrun` command to verify that the installation was successful. This test can take up to 60 minutes. Ensure Space Ranger is in your PATH.

```bash
$ export PATH=/opt/spaceranger-4.1.0:$PATH
$ spaceranger testrun --id=tiny
-----------------------------------------------------------------------------
Running preflight checks (please wait)...
Checking sample info...
Checking FASTQ folder...
Checking reference...

... 

Pipestance completed successfully!

```

--------------------------------

### Copy Slurm Template

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/advanced/cluster-mode

Copy the example Slurm template to create a new configuration file for Space Ranger.

```bash
# command to copy file:
cp -v slurm.template.example slurm.template

# output looks like this:
‘slurm.template.example’ -> ‘slurm.template’

# command to list files
tree -L 2
```

--------------------------------

### Slurm Job Submission Configuration

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/advanced/cluster-mode

Example configuration for Slurm job submission, specifying task and CPU requirements per task.

```bash
#SBATCH --ntasks=1 --cpus-per-task=__MRO_THREADS__
### Alternatively: --ntasks-per-node=__MRO_THREADS__
```

--------------------------------

### View spaceranger count output structure

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/count-cytassist-pex

Example of the console output and file paths generated after a successful pipeline run.

```text
Outputs:
- Run summary HTML:                                  /path/to/Visium_GEX_PEX/outs/web_summary.html
- Outputs of spatial pipeline:
    Slide image annotated with fiducial alignment:                             /path/to/Visium_GEX_PEX/outs/spatial/aligned_fiducials.jpg
    Slide image annotated with detected tissue:                                /path/to/Visium_GEX_PEX/outs/spatial/detected_tissue_image.jpg
    Scale factors for hires and lowres images and fiducial and spot diameters: /path/to/Visium_GEX_PEX/outs/spatial/scalefactors_json.json
    Slide image scaled to 2000px in the largest dimension:                     /path/to/Visium_GEX_PEX/outs/spatial/tissue_hires_image.png
    Slide image scaled to 600px in the largest dimension:                      /path/to/Visium_GEX_PEX/outs/spatial/tissue_lowres_image.png
    RGB brightfield image generated by CytAssist instrument:                   /path/to/Visium_GEX_PEX/outs/spatial/cytassist_image.tiff
    Registration image between CytAssist image and microscope image:           /path/to/Visium_GEX_PEX/outs/spatial/aligned_tissue_image.jpg
    Slide position and tissue status of barcodes CSV:                          /path/to/Visium_GEX_PEX/outs/spatial/tissue_positions.csv
    Per feature Moran's I CSV:                                                 /path/to/Visium_GEX_PEX/outs/spatial/spatial_enrichment.csv
    Fluorescence intensity at spot CSV:                                        null
- Run summary CSV:                                   /path/to/Visium_GEX_PEX/outs/metrics_summary.csv
- BAM:                                               /path/to/Visium_GEX_PEX/outs/possorted_genome_bam.bam
- BAM BAI index:                                     /path/to/Visium_GEX_PEX/outs/possorted_genome_bam.bam.bai
- BAM CSI index:                                     null
- Filtered feature-barcode matrices MEX:             /path/to/Visium_GEX_PEX/outs/filtered_feature_bc_matrix
- Filtered feature-barcode matrices HDF5:            /path/to/Visium_GEX_PEX/outs/filtered_feature_bc_matrix.h5
- Unfiltered feature-barcode matrices MEX:           /path/to/Visium_GEX_PEX/outs/raw_feature_bc_matrix
- Unfiltered feature-barcode matrices HDF5:          /path/to/Visium_GEX_PEX/outs/raw_feature_bc_matrix.h5
- Secondary analysis output CSV:                     /path/to/Visium_GEX_PEX/outs/analysis
- Per-molecule read information:                     /path/to/Visium_GEX_PEX/outs/molecule_info.h5
- Loupe Browser file:                                /path/to/Visium_GEX_PEX/outs/cloupe.cloupe
- Feature Reference:                                 /path/to/Visium_GEX_PEX/outs/feature_reference.csv
- Target Panel file:                                 null
- Probe Set file:                                    /path/to/Visium_GEX_PEX/outs/probe_set.csv
- Normalization factors used to normalize AB counts: /path/to/Visium_GEX_PEX/outs/isotype_normalization_factors.csv
- Deconvolution directory:                           /path/to/Visium_GEX_PEX/outs/deconvolution
- Raw probe barcode matrix:                          /path/to/Visium_GEX_PEX/outs/raw_probe_bc_matrix.h5

Waiting 6 seconds for UI to do final refresh.
Pipestance completed successfully!

2023-04-08 11:47:17 Shutting down.
Saving pipestance info to "Visium_GEX_PEX/Visium_GEX_PEX.mri.tgz"
```

--------------------------------

### PCA Projection Data Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/secondary-analysis-csv

An example of the `projection.csv` file content, showing Barcode and the first 10 Principal Components (PC-1 to PC-10) with their corresponding values.

```csv
Barcode,PC-1,PC-2,PC-3,PC-4,PC-5,PC-6,PC-7,PC-8,PC-9,PC-10
AACACTTGGCAAGGAA-1,4.346822844040275,-9.073988527954281,-3.9348855477667715,4.4143616349096835,0.570902992727801,5.916871998370152,2.480636375841689,-0.06798408872536493,-0.19559617312320177,1.8447556106163412
AACAGGATTCATAGTT-1,-1.615594647200382,-1.4893042055593746,7.5739700779328665,-3.594441916107372,-0.34089358717427726,2.111157673540723,0.7226241085802059,-3.9462479306752436,0.7109160992468775,0.2148672225802757
AACAGGTTATTGCACC-1,11.032392266516446,-8.48766121740853,-3.061209741692746,-1.0179508777455186,-0.3086495689242125,-1.7476955635612388,-4.667269353092443,3.0867661655728873,4.077976646698517,3.4325955564744035
AACAGGTTCACCGAAG-1,0.02261690362615809,-1.1836459670547157,-0.4219683969014265,-0.9704969551004782,0.042818261398003474,0.7016418174052369,0.5984518607384657,0.4370020158231471,5.6108084569945715,-0.5928326084763261
AACAGTCAGGCTCCGC-1,23.551530490594487,1.485566122772231,-4.061849114221165,-3.572810445316029,0.7253401628543874,8.335238428414028,-0.27411229186554853,-1.419600005890016,8.151194312679634,-0.4650714219420635
```

--------------------------------

### Download Space Ranger 1.3.1 (tar.gz)

Source: https://www.10xgenomics.com/support/software/space-ranger/downloads/previous-versions

Use this command to download the Space Ranger 1.3.1 software compressed with tar.gz. Ensure you have curl installed.

```bash
curl -o spaceranger-1.3.1.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-1.3.1.tar.gz?Expires=1776370658&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=ZGgVk6RU63L7UN7r8gyJ05apm5oh0W~-g0w2102BCJ7Pwyx14it1LNqaZScVptFKqBzermD5Qgf7Whb56AfYNKTj1X4VkMug~XvAa1vgXot9M8D7o7wSgDSC4~vxuUSfK8BiczDkNC0alMn0p-YW6-9Rv108MXFsFoSK3K9LuuLvArQrMYojuUkrRs~qkcQ3uZp2reJxdYu02al7yLYfe3VufSZ-NSB7ewcZ2tkqGFw4~ehnjZ7BZBJ9E5iQ89eI4tZRuXbv2CHYc93cYGjbtidgotDdHrN7IhP6llRrr8an1d5pD7p2rQiy2825A4hrennYLyewDkRPBDrMSvCA6Q__"
```

--------------------------------

### Download Space Ranger 2.0.1 (tar.gz)

Source: https://www.10xgenomics.com/support/software/space-ranger/downloads/previous-versions

Use this command to download the Space Ranger 2.0.1 software compressed with tar.gz. Ensure you have curl installed.

```bash
curl -o spaceranger-2.0.1.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.0.1.tar.gz?Expires=1776370658&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=LDdInWKt3E7oJ52HX25mnubckkmYCmivQHs9~2wY7mPz6nluybdrPoDQBE81CvpzuQxcRu7dg0ffsIY0uOYtycdWioUh6nt1iHIP32ZihMN5zbkyNo70amPb3WbyGPuUEhM6rYmtepekV8qLeVc5DYeSsP3fSFUYSE8CPR47Nw2pFzsGEjhaueTcnoCZjZ6CU6beQ~elrX19flvVZ1f95SWPMEKbW1wWba7VeZV3tR3tCxiGM7cQnCH9OSWe5WYj5YYpEMrjg~lPbykvktJX4aHx5ZukS3DYHZPYmqBLfKEI04xA0TwNa-J6KEIb0OELY4tfUOzkl7qtDBDwAdzJzw__"
```

--------------------------------

### Unpack Space Ranger Software

Source: https://www.10xgenomics.com/support/software/space-ranger/downloads/space-ranger-installation

Download and unpack the Space Ranger tar file into your desired directory. This example uses /opt.

```bash
$ cd /opt
[ download file from downloads page ]
$ tar -xzvf spaceranger-4.1.0.tar.gz
```

--------------------------------

### Download Space Ranger 2.0.0 (tar.gz)

Source: https://www.10xgenomics.com/support/software/space-ranger/downloads/previous-versions

Use this command to download the Space Ranger 2.0.0 software compressed with tar.gz. Ensure you have curl installed.

```bash
curl -o spaceranger-2.0.0.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.0.0.tar.gz?Expires=1776370658&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=Agrd715xuvX7kGWKl3ETO6GnG7YcZsomDBZTB~hmN2J6sLfFN8-wToDmwJGDWn4xolv1BTXFsoM9OqHUvtabhGBASs8CHs2s1lAMR7Ac4UDqC800OmpCwFgDgbdTrYmYaioqX9kQU7UiJr3F2ABbpeJ72xhzHZdfQ5Hv7CIF4s2zfRB9aOo0fSMqndqy0XnFC4C-CEEiUCndu-73Y2tRy9HPjcc8KvL4hZu~XRGS67jlFlLdR97owDEeLBxhwgqLtew4U3tMmC7PCPnXBr8uEw9Q1h~3xmhbSWOv337UUIG77ckUy8hvdWWqslZZW0oJ7-RXd~Ewv2AMSBU1hoD9BA__"
```

--------------------------------

### Download Space Ranger 2.1.0 (tar.gz)

Source: https://www.10xgenomics.com/support/software/space-ranger/downloads/previous-versions

Use this command to download the Space Ranger 2.1.0 software compressed with tar.gz. Ensure you have curl installed.

```bash
curl -o spaceranger-2.1.0.tar.gz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.1.0.tar.gz?Expires=1776370658&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=iDK-vXYHS0qWzsbqrZaqYOuWhBxl2a0Fy5Q~NSLeSstwuBZphhrNNmrWwP-Mx0qME61VuJjGFBvZsMVXJooUKgNGUD1-YRrcuQUh6Is1tpzVxoeVyrhkUtqTfULrBfgaNloVArQdbHDqdrAJqVFhinqdyUjIBKj62zYhgCxEJUgUEXTHj92s6UwIy0aU1e1ZbRMcBYHr9564xlxxnx0BfulipnM8~hioj7SqOQFnblfS78DrICNtfURANnTliOPghHVisgiCEzg8pCBTtpV08RJh8cy7DFLVCC-xi15VWlyPfwwW1rS5sgyQTusMlqHyBJ7Q5EtEGFmQ2IF4UJwkyQ__"
```

--------------------------------

### Download Space Ranger 2.1.0 (tar.xz)

Source: https://www.10xgenomics.com/support/software/space-ranger/downloads/previous-versions

Use this command to download the Space Ranger 2.1.0 software compressed with tar.xz. Ensure you have curl installed.

```bash
curl -o spaceranger-2.1.0.tar.xz "https://cf.10xgenomics.com/releases/spatial-exp/spaceranger-2.1.0.tar.xz?Expires=1776370658&Key-Pair-Id=APKAI7S6A5RYOXBWRPDA&Signature=GhCqp0X17WH~~M~K7JJtMTZa0eWJoticsHstTG3l77yNIsUNwWBpCr2VOE0q61o9rXl0qn-GR5pbqB~bPPcou7uTRbWjamLucGDnWUSiIrXJpbgIVXyOCLEKSC4CGL4L2DVOq9QhCunGkBIwTj3Jj974iuZsJpnpP8uqimeYe9Ui84y7GXPZYYRUatZTAqgduOP4HZWQrfQlBSYaphCMCNo6~FwCbNzcFQJ7aW8d4x6~9nuhmoai2UM~WGcbSMdqLqpblpIOT8iCxwCDY5VeYOf4YKvM6XNm8v7D-G2NEtlMjIkKKkAw20hNpyEXxYd0jcJNEiZz7R7lHU53wjFIKQ__"
```

--------------------------------

### Space Ranger Folder Structure

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/tutorials/setup-spaceranger

This is a hierarchical view of the Space Ranger installation directory, highlighting key subfolders and their contents. No specific setup is required to view this structure.

```bash
1spaceranger-2.0.0
2├── bin
3├── external
4│   ├── anaconda
5│   ├── martian
6│   │     └── jobmanagers
7│   ├── spaceranger_tiny_inputs
8│   └── spaceranger_tiny_ref
9├── lib
10│   ├── bin
11│   │     ├── bamtofastq
12│   │     ├── redstone
13│   │     └── ...
14│   └── python
15│       └── cellranger
16│           └── barcodes
17│               ├── visium-v1_coordinates.txt
18│               ├── visium-v2_coordinates.txt
19│               ├── visium-v4_coordinates.txt
20│               ├── visium-v5_coordinates.txt
21│               └── ...
22├── mro
23├── probe_sets
24│   ├── Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A.csv
25│   ├── Visium_Human_Transcriptome_Probe_Set_v2.0_GRCh38-2020-A.csv
26│   └── Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv
27├── target_panels
28│   ├── gene_signature_v1.0_GRCh38-2020-A.target_panel.csv
29│   ├── immunology_v1.0_GRCh38-2020-A.target_panel.csv
30│   ├── neuroscience_v1.0_GRCh38-2020-A.target_panel.csv
31│   └── pan_cancer_v1.0_GRCh38-2020-A.target_panel.csv
32└── THIRD-PARTY-LICENSES.spaceranger.txt

```

--------------------------------

### Feature Dispersion Data Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/secondary-analysis-csv

An example of the `dispersion.csv` file content, showing Feature (Ensembl ID) and its corresponding Normalized Dispersion value.

```csv
Feature,Normalized.Dispersion
ENSG00000187634,0.6831683505253648
ENSG00000188976,-0.14721475503619233
ENSG00000187961,2.2333235330589933
ENSG00000187583,-0.1377803092462445
ENSG00000187642,-0.4131854711145404
ENSG00000188290,-0.6689923111662834
ENSG00000187608,-1.0069025521553716
ENSG00000188157,0.1691687357833229
ENSG00000237330,2.0109141055507394
ENSG00000131591,-1.4170406794742954
ENSG00000162571,2.501396789174146
```

--------------------------------

### Selected Features for PCA Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/secondary-analysis-csv

An example of the `features_selected.csv` file content, showing a list of features identified by an index and their corresponding Ensembl IDs.

```csv
Feature
1        ENSMUSG00000114038
2        ENSMUSG00000058063
3        ENSMUSG00000087216
4        ENSMUSG00000085244
5        ENSMUSG00000021604
```

--------------------------------

### Run system sitecheck

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/tutorials/setup-spaceranger

Executes the sitecheck command and redirects output to a text file for review.

```bash
spaceranger sitecheck > sitecheck.txt
```

--------------------------------

### Download Reference Genomes

Source: https://www.10xgenomics.com/support/software/space-ranger/downloads

Use these commands to download pre-built reference datasets for common organisms.

```bash
curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38-2024-A.tar.gz"
```

```bash
curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCm39-2024-A.tar.gz"
```

```bash
curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mRatBN7-2-2024-A.tar.gz"
```

```bash
curl -O "https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-GRCh38_and_GRCm39-2024-A.tar.gz"
```

--------------------------------

### Download Visium HD Tiny Mouse Brain Dataset via CLI

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/resources/visium-hd-example-data

Use curl to download the downsampled dataset for testing Space Ranger output formats.

```bash
# Visium HD 3' Tiny Mouse Brain Dataset
curl -O https://cf.10xgenomics.com/samples/spatial-exp/4.0.1/Visium_HD_Tiny_3prime_Dataset/Visium_HD_Tiny_3prime_Dataset_outs.zip
```

--------------------------------

### Download dataset files with wget

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/tutorials/count-ff-tutorial

Alternative method using wget to download required FASTQ and image files into the datasets directory.

```bash
# Create datasets folder
mkdir datasets

# Download FASTQ to datasets folder
wget -P datasets/ https://s3-us-west-2.amazonaws.com/10x.files/samples/spatial-exp/1.1.0/V1_Adult_Mouse_Brain/V1_Adult_Mouse_Brain_fastqs.tar

# Download image file to datasets folder
wget -P datasets/ https://cf.10xgenomics.com/samples/spatial-exp/1.1.0/V1_Adult_Mouse_Brain/V1_Adult_Mouse_Brain_image.tif

# Expected output
Resolving s3-us-west-2.amazonaws.com (s3-us-west-2.amazonaws.com)... 52.218.217.16
Connecting to s3-us-west-2.amazonaws.com (s3-us-west-2.amazonaws.com)|52.218.217.16|:443...
connected.
HTTP request sent, awaiting response... 200 OK
Length: 28987985920 (27G) [application/x-tar]
Saving to: ‘V1_Adult_Mouse_Brain_fastqs.tar’

10% [=======>                                          ] 3,179,419,763 36.2MB/s  eta 11m 35s
```

--------------------------------

### List Job Manager Templates

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/advanced/cluster-mode

Navigate to the Martian runtime's job managers directory and list the available template files.

```bash
cd /opt/spaceranger-2.1.0/external/martian/jobmanagers
tree -L 2
```

--------------------------------

### Pan-Human Azimuth Model CSV Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/space-ranger-annotate-outputs

Example content for a Pan-Human Azimuth model CSV file showing hierarchical cell type annotations and probabilistic scores.

```csv
barcode,broad_cell_type,coarse_cell_type,fine_cell_type,full_hierarchical_labels,final_level_softmax_prob,coarse_cell_type_unfiltered,umi_count
cellid_000000023-1,Epithelial cell,Epithelial cell of lung,Club cell,Epithelial cell|Epithelial cell of lung|Club cell,0.72484344,Epithelial cell of lung,1404
cellid_000000024-1,Epithelial cell,Epithelial cell of lung,Club cell,Epithelial cell|Epithelial cell of lung|Club cell,0.46240065,Epithelial cell of lung,1482
cellid_000000026-1,Epithelial cell,Epithelial cell of breast,Mammary luminal cell,Epithelial cell|Epithelial cell of breast|Mammary luminal cell|PIP mammary luminal cell,0.9022441,Epithelial cell of breast,1206
```

--------------------------------

### Restart Pipestance from Beginning

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/sr-troubleshooting

To restart a pipestance from scratch, move the existing output directory to a new location.

```bash
mv HAWT7ADXX HAWT7ADXX.old
```

--------------------------------

### GeoJSON Polygon FeatureCollection Example

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/segmentation-inputs

This is an example of a GeoJSON FeatureCollection containing polygon data, suitable for cell or nuclei outlines. Ensure the 'type' is 'FeatureCollection' and each feature has a 'geometry' object with 'type' as 'Polygon' and 'coordinates'.

```json
{
   "type": "FeatureCollection",
   "features": [
     {
       "type": "Feature",
       "id": "12059192-3b27-4438-96dc-97b41ca84717",
       "geometry": {
         "type": "Polygon",
         "coordinates": [
           [
             [3418.94, 2],
             [3414.62, 3.85],
             [3414.12, 22.65],
             [3415.06, 27.26],
             [3420.1, 35.15],
             [3428.03, 40.22],
             [3437.01, 42.94],
             [3440.69, 45.87],
             [3445.32, 46.71],
             [3468.85, 46.71],
             [3477.88, 44.35],
             [3534.35, 44.31],
             [3546.79, 37.83],
             [3552.28, 30.11],
             [3552.94, 25.45],
             [3552.93, 6.63],
             [3550.68, 2.49],
             [3546, 2],
             [3418.94, 2]
           ]
         ]
       }
     }
   ]
}
```

--------------------------------

### Define Libraries CSV structure

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/count-cytassist-pex

Example of a CSV file structure for specifying GEX and PEX library inputs.

```csv
fastqs| sample| library_type  
---|---|---  
/path/to/GEX_FASTQs| GEX_sample1| Gene Expression  
/path/to/PEX_FASTQs| Ab_sample1| Antibody Capture
```

--------------------------------

### CLI Command: spaceranger mkfastq

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/command-line-arguments

Executes the demultiplexing pipeline on Illumina BCL run folders using specified sample sheets and configuration options.

```APIDOC
## CLI Command: spaceranger mkfastq

### Description
Runs the Illumina demultiplexer on sample sheets containing 10x-specific sample index sets and generates quality metrics. Note: This pipeline is deprecated.

### Usage
`spaceranger mkfastq --run=PATH [options]`

### Parameters
#### Required Parameters
- **--run** (PATH) - Required - Path of Illumina BCL run folder.

#### Optional Parameters
- **--id** (NAME) - Optional - Name of the folder created by mkfastq.
- **--csv / --samplesheet / --sample-sheet** (PATH) - Optional - Path to the sample sheet.
- **--force-single-index** (FLAG) - Optional - Allow demultiplex using i7 half of the index pair.
- **--filter-single-index** (FLAG) - Optional - Only demultiplex i7-only samples.
- **--filter-dual-index** (FLAG) - Optional - Only demultiplex i7/i5 dual-indexed samples.
- **--rc-i2-override** (BOOL) - Optional - Override for I2 read reverse complement detection.
- **--delete-undetermined** (FLAG) - Optional - Delete Undetermined FASTQ files.
- **--output-dir** (PATH) - Optional - Folder where FASTQs and reports are generated.
- **--project** (NAME) - Optional - Custom project name.
- **--jobmode** (MODE) - Optional - Job manager (local, sge, lsf, or .template).
- **--localcores** (NUM) - Optional - Max cores for local jobs.
- **--localmem** (NUM) - Optional - Max GB memory for local jobs.
- **--uiport** (PORT) - Optional - Port for web UI.
- **--nopreflight** (FLAG) - Optional - Skip preflight checks.
```

--------------------------------

### BCL Convert Sample Sheet Configuration

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/inputs/fastqs-demultiplexing-with-illumina-software

Configure the sample sheet for BCL Convert to not generate FASTQ files for indices, as Space Ranger does not require them. Ensure `CreateFastqForIndexReads` is set to 0.

```csv
[Header]
FileFormatVersion,2

[BCLConvert_Settings]
CreateFastqForIndexReads,0
TrimUMI,0

[BCLConvert_Data]
Lane,Sample_ID,index,index2
1,test_sample,GTAACATGCG,AGGTAACACT

```

--------------------------------

### Define LSF job template

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/advanced/cluster-mode

Example template for LSF clusters using the __MRO_MEM_MB__ variable to specify memory in megabytes.

```bash
cat bsub.template

## Expected output
#BSUB -J __MRO_JOB_NAME__
#BSUB -n __MRO_THREADS__
#BSUB -o __MRO_STDOUT__
#BSUB -e __MRO_STDERR__
#BSUB -R "rusage[mem=__MRO_MEM_MB__]"
#BSUB -R span[hosts=1]

__MRO_CMD__
```

--------------------------------

### Define SGE job template

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/advanced/cluster-mode

Example template for SGE clusters using the mem_free resource to manage memory allocation.

```bash
cat sge.template

## Expected output
#$ -N __MRO_JOB_NAME__
#$ -V
#$ -pe threads __MRO_THREADS__
#$ -l mem_free=__MRO_MEM_GB__G
#$ -cwd
#$ -o __MRO_STDOUT__
#$ -e __MRO_STDERR__

__MRO_CMD__
```

--------------------------------

### Prepare a reference with spaceranger mkref

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/running-pipelines/command-line-arguments

Generates a reference for 10x analysis software using a GTF and FASTA file.

```bash
spaceranger mkref [OPTIONS] --genome <GENOME_NAMES> --fasta <FASTA_FILES> --genes <GTF_FILES>
```

--------------------------------

### Extract Sample FASTQ Files

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/tutorials/count-cytassist-tma

Extracts sample FASTQ files from a tar archive and removes the archive. Ensure the `datasets` directory exists.

```bash
# Extract sample FASTQ files
tar -xvf datasets/CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_fastqs.tar -C datasets/ && rm datasets/CytAssist_11mm_FFPE_Mouse_TMA_3x3_2mm_fastqs.tar
```

--------------------------------

### Barcode mappings CSV structure

Source: https://www.10xgenomics.com/support/software/space-ranger/latest/analysis/outputs/segmented-outputs

Example of the CSV structure for barcode mappings showing relationships between different bin sizes and cell IDs.

```csv
Square_002um,Square_008um,Square_016um,Cell_id,In_nucleus,In_cell
s_002um_00000_00000,s_008um_00000_00000,s_016um_00000_00000,cellid_000000000,false,false
s_002um_00000_00001,s_008um_00000_00000,s_016um_00000_00000,cellid_000000000,false,false
S_002um_00000_00002,s_008um_00000_00000,s_016um_00000_00000,cellid_000199028,false,true
```