10x Genomics
Single Cell Gene Expression

Cell Ranger, printed on 04/23/2024

Release Notes for Cell Ranger 2.1 Gene Expression

Cell Ranger 2.1.1 Gene Expression

Note: This is expected to be the last version of Cell Ranger to support CentOS/RedHat 5 and Ubuntu 10. If you are using one of those operating systems, Cell Ranger will now warn you. Future versions of Cell Ranger will require CentOS/RedHat 6 or Ubuntu 12 or later. See the 10x OS Support page for further information.

Bug Fixes

• Fix library ID labels being out of order in the matrix HDF5 file produced by cellranger aggr when 10 or more libraries are aggregated. This manifests as Loupe Cell Browser showing the library ID labels out of order after running cellranger reanalyze.
• Fix an out-of-memory error occurring when generating the kmer index on a reference with very long transcripts, e.g. on a pre-mRNA reference used when analyzing nuclei samples.
• Fix crash when analyzing FASTQs produced by SRA's fastq-dump.
• Fix the Differential Expression table in the web summary disappearing when gene IDs are equal to gene names in the reference GTF.
• Fix a few web summary metrics becoming negative when more than 2.1 billion reads are analyzed at once.
• Fix incorrect parsing of the --localcores argument, causing --localmem to be ignored when specified immediately after --localcores.
• Fix crash in mkfastq on NovaSeq when RunParameters.xml is named runParameters.xml.
• Fix hang when running sitecheck on some systems.
• Fix error reporting in python stage code imports.
• Fix estimation of stage virtual memory usage.

Improvements

• Truncate large metadata files when generating a tarball for upload to 10x, rather than omitting them.
• Remove the requirement that the reference FASTA file modification time precede the STAR index file modification times.
• The default --localmem in cluster mode will no longer ever be more than the free memory available when the cellranger starts.

Cell Ranger 2.1.0 Gene Expression

New Features

• Add support for and autodetection of Single Cell 5' gene expression libraries, with support for both paired-end alignment (150x150) and R2-only alignment (26x98).
• Add --r1-length and --r2-length options to cellranger count which enable hard trimming of input FASTQs.
• Add --exclude-genes option to cellranger reanalyze which, analogously to --genes, allows for the exclusion of some genes from the secondary analysis (PCA, clustering, etc.).
• Add --chemistry to cellranger count to override the automatic chemistry detection.

Performance Improvements

• Reduce the run time by 30%.
• Reduce the disk storage high-water-mark by 60%.

Algorithm Improvements

• Change the Antisense Reads Metric to only count a read as antisense if it has no sense alignments, effectively prioritizing sense alignments over antisense for this computation.

Output File Changes

• Stop generating the TR and TQ BAM tags because these tags were retaining trimmed sequences that Cell Ranger would ignore anyway after converting the BAM back to FASTQ.
• Add more mapping metrics (Reads Mapped to Genome, Reads Mapped Confidently to Genome), and reorder the mapping metrics to be consistent with their order of computation.

Bug Fixes

• Fix mkfastq allowing max bcl2fastq threads to exceed --localcores.
• Fix mkfastq crashing when reading NovaSeq quality data from RTA 3.3 and later.
• Fix excessive memory requests in SC_RNA_ANALYZER.
• Fix nondetection of louvain binary failure in RUN_GRAPH_CLUSTERING.
• Fix crash in RUN_GRAPH_CLUSTERING when /dev/stdin doesn't exist.
• Fix the barcode rank plot concatenating instead of unioning barcodes in multi-genome datasets.

System Requirements Changes

• Cell Ranger no longer supports Ubuntu 8 or CentOS 5.2 Linux distributions. Ubuntu 10.04 LTS or CentOS 5.5 or greater are now required.

Job Scheduling

• The pipeline management system, mrp, is now open source on GitHub.
• The monitoring port for the user interface is now always on by default, with an OS-selected port if none is specified.
  • This behavior can be disabled with --disable-ui.
  • Access to the user interface port, if no port was specified explicitly, now requires a randomly-generated authentication token. This token is visible in the pipeline standard output and in the _uiport file.
• A new tool, mrstat is now available.
  • Given the path to the directory with a running pipeline, mrstat will return basic information about the progress of the pipeline.
  • With the --stop flag, it will cause the pipeline to fail and exit.
• Two new variables are available for use in cluster-mode templates:
  • __MRO_JOB_WORKDIR__ can be used to specify the absolute path to the directory where the job should execute. This should alleviate issues on clusters such as PBS which sometimes do not set the working directory correctly.
  • __MRO_ACCOUNT__ passes the MRO_ACCOUNT environment variable from mrp's environment. This is intended for cluster managers which support charging resources to specific accounts.
• The pipeline standard output and log will now periodically provide progress updates for in-progress stages.
• mrp will now provide more clear and useful error reporting when the pipeline directory runs out of disk space.
• Several enhancements to the reliability of pipeline restart.
• Fixes for several cases where a pipeline could "hang" indefinitely without making further progress.
• Pipelines should now do a better job of staying within their CPU usage allocation.