Cell Ranger ARC2.0 (latest), printed on 07/06/2022
The Illumina NovaSeq control software v1.8 upgrade affects cellranger-arc mkfastq's ability to autodetect the i5 (Index 2) orientation due to Illumina's reagent name changes in the recipe XML file. This results in all GEX reads going into Undetermined and there will be no error. ATAC reads are unaffected. Several solutions to fix this issue are provided on this Knowledge Base article.
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The cellranger-arc workflow starts by demultiplexing the Illumina sequencer's base call files (BCLs) for each flow cell directory (ATAC or Gene Expression) into FASTQ files. 10x Genomics has developed cellranger-arc mkfastq, a pipeline that wraps Illumina's bcl2fastq and provides a number of convenient features in addition to the features of bcl2fastq:
--use-bases-mask.The Multiome ATAC library is single-indexed while the Multiome GEX library is
dual-indexed. cellranger-arc mkfastq can auto-detect the
type of flow cell based on the length of the i5 index read and selects the
appropriate mode depending on the sample indexes used, and enables index-hopping
filtering automatically for dual-indexed flow cells. For example, a Multiome GEX
library prepared with the Dual Index Kit TT Set A, well A1 can be specified in
the samplesheet as SI-TT-A1, and cellranger-arc mkfastq
will recognize the i7 and i5 indices as GTAACATGCG and AGTGTTACCT,
respectively. Similarly for a Multiome ATAC library prepared with Single Index
Kit N Set A, well A1 can be specified in the samplesheet as SI-NA-A1, and
cellranger-arc mkfastq will recognize the four i7 indexes
AAACGGCG, CCTACCAT, GGCGTTTC, and TTGTAAGA and merge the resulting FASTQ
files.
The compute workflow begins with running one instance of cellranger-arc mkfastq for each flow cell of data being analyzed. The same command cellranger-arc mkfastq can be used to demultiplex ATAC and GEX flow cells. Once the ATAC flow cell(s) and GEX flow cell(s) are successfully demultiplexed, one instance of cellranger-arc count is run for each paired Multiome ATAC and GEX library; independent of the number of sequencing runs of each library. Specific examples are described below.
In this example, a Multiome ATAC library (with sample index SI-NA-A1) and a Multiome GEX library (with sample index SI-TT-A1) were processed on different flow cells. The GEX library was processed on lane 1 of its flow cell, whereas the ATAC library was processed on lane 2 of its flow cell. Then, a separate instance of cellranger-arc mkfastq is run for each library, and all resultant FASTQ files are processed though a single instance of cellranger-arc count.
In this example, one Multiome ATAC library with sample index SI-NA-A1
was sequenced on two flow cells. The cellranger-arc count pipeline cannot process ATAC libraries alone.
In this example, two Multiome GEX libraries (each processed through a
separate GEM well with sample indices SI-TT-A1 and SI-TT-A2)
are multiplexed on a single flow cell. GEX Library 1 was processed on lane 1 and GEX Library 2 was processed on lane 2 of the same flow cell. The cellranger-arc count pipeline cannot process GEX libraries alone.
The cellranger-arc mkfastq pipeline accepts additional options beyond
those shown in the table below because it is a wrapper around
bcl2fastq. Consult the User Guide for Illumina's
bcl2fastq
for more information.
| Parameter | Function |
|---|---|
--run | Required. The path of Illumina BCL run folder. |
--id | Optional; defaults to the name of the flow cell referred to by --run. Name of the folder created by mkfastq. |
--samplesheet | Optional. Path to an Illumina Experiment Manager-compatible samplesheet which contains 10x Genomics sample index names (e.g., SI-NA-A1 or SI-TT-A12) in the sample index column. All other information, such as sample names and lanes, should be in the samplesheet. |
--sample-sheet | Optional. Equivalent to --samplesheet above. |
--csv | Optional. Path to a simple CSV with lane, sample, and index columns, which describe the way to demultiplex the flow cell. The index column should contain a 10x Genomics sample dual-index name (e.g., SI-TT-A12). This is an alternative to the Illumina IEM samplesheet, and will be ignored if --samplesheet is specified. |
--simple-csv | |
--lanes | bcl2fastq option. Comma-delimited series of lanes to demultiplex (e.g. 1,3). Use this if you have a samplesheet for an entire flow cell but only want to generate a few lanes for further 10x Genomics analysis. |
--use-bases-mask | bcl2fastq option. Same meaning as for bcl2fastq. Use to clip extra bases off a read if you ran extra cycles for QC. |
--delete-undetermined | bcl2fastq option. Delete the Undetermined FASTQs generated by bcl2fastq. Useful if you are demultiplexing a small number of samples from a large flow cell. |
--output-dir | bcl2fastq option. Generate FASTQ output in a path of your own choosing, instead of flow_cell_id/outs/fastq_path. |
--project | bcl2fastq option. Custom project name, to override the samplesheet or to use in conjunction with the --csv argument. |
--jobmode | Martian option. Job manager to use. Valid options: local (default), sge, lsf, slurm or a .template file. |
--localcores | Martian option. Set max cores the pipeline may request at one time. Only applies when --jobmode=local. |
--localmem | Martian option. Set max GB the pipeline may request at one time. Only applies when --jobmode=local. |
The cellranger-arc mkfastq pipeline recognizes two file formats for
describing samples: a simple, three-column CSV format, and the Illumina
Experiment Manager (IEM) samplesheet format used by bcl2fastq. Both these formats are illustrated with a Multiome ATAC flow cell and Multiome GEX flow cell example.
The example (tiny-bcl-atac) dataset is solely designed to demo the cellranger-arc mkfastq pipeline. It cannot be used to run downstream pipelines (e.g. cellranger-arc count).
To follow along, do the following:
cellranger-arc-tiny-bcl-atac-1.0.0.tar.gz and
cellranger-arc-tiny-bcl-gex-1.0.0.tar.gz tar files in a convenient location.A simple CSV sample sheet is recommended for most sequencing experiments.
The simple CSV format has only three columns (Lane, Sample, Index), and is thus
less prone to formatting errors. You can see an example of this in
cellranger-arc-tiny-bcl-atac-simple-1.0.0.csv:
Lane,Sample,Index 1,test_sample_atac,SI-NA-A1
and in cellranger-arc-tiny-bcl-gex-simple-1.0.0.csv:
Lane,Sample,Index 1,test_sample_gex,SI-TT-A1
Here are the options for each column:
| Lane | Which lane(s) of the flow cell to process. Can be either a single lane, a range (e.g., 2-4) or '*' for all lanes in the flow cell. |
| Sample | The name of the sample. This name is the prefix to all the generated FASTQs, and corresponds to the --sample argument in all downstream 10x Genomics pipelines.Sample names must conform to the Illumina bcl2fastq naming requirements. Only letters, numbers, underscores and hyphens area allowed; no other symbols, including dots (".") are allowed. |
| Index | The 10x Genomics sample index that was used in library construction, e.g., SI-TT-A1 for a Dual-Indexed Multiome GEX library, or SI-NA-A1 for a Multiome ATAC library. |
To run cellranger mkfastq with a simple layout CSV, use the --csv
argument. Here's how to run cellranger mkfastq on the
tiny-bcl-atac sequencing run with the simple layout:
$ cellranger-arc mkfastq --id=tiny-bcl-atac \ --run=/path/to/cellranger-arc-tiny-bcl-atac-1.0.0 \ --csv=/path/to/cellranger-arc-tiny-bcl-atac-simple-1.0.0.csv cellranger-arc mkfastq (2.0.1) Copyright (c) 2020 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Martian Runtime - v4.0.5 Running preflight checks (please wait)... yyyy-mm-dd hh:mm:ss [runtime] (ready) ID.tiny-bcl-atac.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET yyyy-mm-dd hh:mm:ss [runtime] (split_complete) ID.tiny-bcl-atac.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET yyyy-mm-dd hh:mm:ss [runtime] (run:local) ID.tiny-bcl-atac.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET.fork0.chnk0.main yyyy-mm-dd hh:mm:ss [runtime] (chunks_complete) ID.tiny-bcl-atac.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET ...
The cellranger-arc mkfastq pipeline can also be run with a sample sheet in the Illumina Experiment Manager (IEM) format. Use this format if you did not sequence with sample indices. An IEM sample sheet consists of a number of fields specific to running on Illumina platforms, and a [Data] section. The sample, lane and index information goes in the [Data] section.
Example [Data] section for a dual-indexed Multiome GEX flow cell:
[Data] Lane,Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,I5_Index_ID,index2,Sample_Project,Description 1,s1,test_sample,,,SI-TT-A1,SI-TT-A1,SI-TT-A1,SI-TT-A1,p1,
Here, SI-TT-A1 refers to a 10x Genomics dual-indexed library sample index.
In this example, only reads from lane 1 will be used. To demultiplex the given
sample index across all lanes, omit the lanes column entirely.
Example [Data] section for a single-indexed Multiome ATAC flow cell:
[Data] Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description s1,test_sample_miseq,,,SI-NA-A1,SI-NA-A1,p1,
Here, SI-NA-A1 refers to a 10x Genomics single-indexed sample index, a set of
four oligo sequences. cellranger-arc mkfastq also supports
listing oligo sequences explicitly.
Sample names must conform to the Illumina bcl2fastq naming requirements. Only letters, numbers, underscores, and hyphens are allowed. No other symbols, including dots ("."), are allowed.
Also note that while an authentic IEM samplesheet will contain other sections above the [Data] section, these are optional for demultiplexing. For demultiplexing an existing run with cellranger-arc mkfastq, only the [Data] section is required.
Next, run the cellranger-arc mkfastq pipeline, using the --samplesheet argument:
$ cellranger-arc mkfastq --id=tiny-bcl-atac \ --run=/path/to/tiny-bcl-atac \ --samplesheet=cellranger-arc-tiny-bcl-atac-samplesheet-1.0.0.csv cellranger-arc mkfastq (2.0.1) Copyright (c) 2020 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Martian Runtime - v4.0.5 Running preflight checks (please wait)... yyyy-mm-dd hh:mm:ss [runtime] (ready) ID.tiny-bcl-atac.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET yyyy-mm-dd hh:mm:ss [runtime] (split_complete) ID.tiny-bcl-atac.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET yyyy-mm-dd hh:mm:ss [runtime] (run:local) ID.tiny-bcl-atac.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET.fork0.chnk0.main yyyy-mm-dd hh:mm:ss [runtime] (chunks_complete) ID.tiny-bcl-atac.MAKE_FASTQS_CS.MAKE_FASTQS.PREPARE_SAMPLESHEET ...
If you encounter any preflight errors, refer to the Troubleshooting page.
Once the cellranger-arc mkfastq pipeline has successfully
completed, the output can be found in a new folder named with the value
provided to cellranger-arc mkfastq in the --id option
(if not specified, defaults to the name of the flow cell):
$ cellranger-arc mkfastq --id=tiny-bcl-atac \ --run=/path/to/tiny-bcl-atac \ --samplesheet=cellranger-arc-tiny-bcl-atac-samplesheet-1.0.0.csv cellranger-arc mkfastq (2.0.1) Copyright (c) 2020 10x Genomics, Inc. All rights reserved. ------------------------------------------------------------------------------- Martian Runtime - v4.0.5 ... Pipestance completed successfully! yyyy-mm-dd hh:mm:ss Shutting down. Saving pipestance info to "tiny-bcl-atac/tiny-bcl-atac.mri.tgz" $ ls -l drwxrwxr-x 4 jdoe jdoe 4096 Aug 29 15:29 tiny-bcl-atac
The key output files can be found in outs/fastq_path, and are
organized in the same manner as a conventional bcl2fastq run:
$ ls -l tiny-bcl-atac/outs/fastq_path/ total 31744 drwxrwxr-x 3 jdoe jdoe 24 Sep 7 22:49 p1 drwxrwxr-x 3 jdoe jdoe 26 Sep 7 22:48 Reports drwxrwxr-x 2 jdoe jdoe 193 Sep 7 22:48 Stats -rw-rw-r-- 1 jdoe jdoe 3806257 Sep 7 22:48 Undetermined_S0_L001_I1_001.fastq.gz -rw-rw-r-- 1 jdoe jdoe 967448 Sep 7 22:48 Undetermined_S0_L001_R1_001.fastq.gz -rw-rw-r-- 1 jdoe jdoe 5773976 Sep 7 22:48 Undetermined_S0_L001_R2_001.fastq.gz -rw-rw-r-- 1 jdoe jdoe 12635207 Sep 7 22:48 Undetermined_S0_L001_R3_001.fastq.gz $ tree tiny-bcl-atac/outs/fastq_path/tiny-bcl-atac/ tiny-bcl-atac/outs/fastq_path/p1 └── s1 ├── test_sample_miseq_S1_L001_I1_001.fastq.gz ├── test_sample_miseq_S1_L001_R1_001.fastq.gz ├── test_sample_miseq_S1_L001_R2_001.fastq.gz └── test_sample_miseq_S1_L001_R3_001.fastq.gz
This example was produced with a samplesheet that included p1 as the Sample_Project, so the directory containing the sample folders is named p1. If a Sample_Project wasn't specified, or if a simple layout CSV file was used (which does not have a Sample_Project column), the directory containing the sample folders would be named according to the flow cell ID instead.
To remove the Undetermined FASTQs from the output, you can run mkfastq with the
--delete-undetermined flag. To see all
cellranger-arc mkfastq options, run
cellranger-arc mkfastq --help.
If the pipeline crashes while running cellranger-arc
mkfastq, upload this tarball (with the extension .mri.tgz) found in your output
directory:
cellranger-arc upload [email protected]
jobid.mri.tgz
where jobid is what you input into the --id option of
mkfastq (if not specified, defaults to the ID of the flow cell). Remember to replace the code in red with your email ID.
This tarball
contains numerous diagnostic logs that we can use for debugging.
You will receive an automated email from 10x Genomics. If not, email [email protected] For the fastest service, respond with the following: