Cell Ranger ARC2.0, printed on 02/21/2024
Undetermined/ because the orientation of i5 (Index2) could not be autodetected.
Changed the duplicate marking algorithm:
Improved computational performance:
aggr pipeline to aggregate multiple libraries from multiple GEM
reanalyze pipeline to enable customized
Changed cell caller override: when
--min-gex-count=Y is specified we choose all barcodes with atac count >= X
and (previously or) gex count >= Y.
The raw feature barcode matrix now only contains barcodes with at least one ATAC count or one GEX count; previously, all allowed barcodes were present.
Change in barcode error correction: correct Hamming distance 1 errors (previously 2).
Added header lines beginning with
# to the fragments.tsv.gz and peaks.bed
files that contain version, reference and sample information.
Change to ATAC peak annotation TSV format:
peak column is now split into three columns:
; separators in the same row.
Improvements to reference construction:
mkref and preflight
count. Previously, it was possible to pass checks in
fail checks in
Eliminated secondary alignments from the position-sorted BAM.
Loupe browser files generated by the pipeline can only be opened by Loupe browser version 5.0 or later.
Increases the upper limit on primary contigs (those that have at least one gene annotation) from 100 to 500. The pipeline will error out if more than 1000 total contigs are present in the reference.
Disables multithreading in mkref to address an issue where mkref would fail on hardware without AVX support. This will be fixed in a future release.
Creates cellranger-arc count for the analysis of 10x Chromium Single Cell Multiome ATAC + Gene Expression data generated from a single GEM well.
Creates cellranger-arc mkfastq for demultiplexing of ATAC or GEX flow cell data for analysis.
Creates cellranger-arc mkref to construct reference packages for use with cellranger-arc count starting with a reference FASTA file and a gene annotations GTF file.
Note: the software cannot be used for the analysis of 10x Chromium Single Cell ATAC, 10x Chromium Single Cell 3' Gene Expression data, or for any kind of joint analysis of the two.