Cell Ranger DNA1.1, printed on 12/21/2024
| Analysis software for the 10x Genomics single cell DNA product is no longer supported. Raw data processing pipelines and visualization tools are available for download and can be used for analyzing legacy data from 10x Genomics kits in accordance with our end user licensing agreement without support. |
The cellranger-dna bamslice command filters the position-sorted BAM file produced by a cellranger-dna cnv run to a subset of cells specified with a custom configuration CSV.
These are the most common command line arguments (run cellranger-dna bamslice --help for a full list):
| Argument | Description |
|---|---|
--id=ID | A unique run ID string: e.g. tumor_primary_subset1 |
--csv=CSV | Path of CSV file containing barcode subset definitions (see Configuration). |
--bam=BAM | Path of BAM file to filter (an output of cellranger-dna cnv). |
After specifying these input arguments, run cellranger-dna bamslice. In this example, we're filtering the outputs of a mixed tumor sample:
$ cd /home/jdoe/runs
$ ls -1 tumor_mixed/outs/*.bam # verify the input file exists
tumor_mixed/outs/possorted_bam.bam
$ cellranger-dna bamslice --id=tumor_subsets \
--csv=tumor_subsets.csv \
--bam=/home/jdoe/runs/tumor_mixed/outs/possorted_bam.bam
The pipeline will begin to run, creating a new folder named with the ID you specified (e.g. /home/jdoe/runs/tumor_subsets) for its output. If this folder already exists, cellranger-dna will assume it is an existing pipestance and attempt to resume running it.
A successful run should conclude with a message similar to this:
2019-05-07 10:20:51 [runtime] (chunks_complete) ID.tumor_subsets.SUBSET_BAM._SUBSET_BAM 2019-05-07 10:20:51 [runtime] (run:local) ID.tumor_subsets.SUBSET_BAM._SUBSET_BAM.fork0.join 2019-05-07 10:20:53 [runtime] (join_complete) ID.tumor_subsets.SUBSET_BAM._SUBSET_BAM Outputs: - subsets: /home/jdoe/runs/tumor_subsets/outs/subsets Pipestance completed successfully!
$ ls -1 tumor_subsets/outs/subsets/*.bam normal.bam tumor_primary.bam
Refer to the BAM page for a description of the output BAM files.
You select your barcodes of interest for each group directly, using a separate barcodes file for each group.
A text editor or Excel may be used to construct the configuration CSV. Your spreadsheet may look something like this:
| A | B | |
|---|---|---|
| 1 | library_id | barcodes_csv |
| 2 | normal | /home/jdoe/normal_barcodes.csv |
| 3 | tumor_primary | /home/jdoe/tumor_primary_barcodes.csv |
When you save this to CSV, it will look something like this:
library_id,barcodes_csv normal,/home/jdoe/normal_barcodes.csv tumor_primary,/home/jdoe/tumor_primary_barcodes.csv
The barcodes CSV files will each have one barcode entry per line, including the GEM well suffix (see GEM wells). Each such file will look something like:
AAACGGGTCAAAGTGA-1 AAAGATGCAATGGGAC-1 ... TTTGTCATCCGCACGA-1