search

10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
Other
340 stars 91 forks source link

CellRanger3 vs CellRanger5 deviating results for annotation of TRA and TRB in VDJ #200

Closed Close-your-eyes closed 8 months ago

Close-your-eyes commented 1 year ago

Dear all,

it happened to me that we mapped the same data 10X VDJ data from human T cells with CellRanger3 and CellRanger5 to a hg38 reference. I noticed that in CellRanger5 much less cells are annotated with TR chains. So, filtering must have become stricter. Okay.

Apart from that, some cells (barcodes) have been annotated with completely different CDR3s (TRA and TRB) and accordingly with different underlying contig sequences.

I am referring to data from filtered_contig_annotations.csv and filtered_contig.fasta.

Is this known? Is it expected? How can that be explained?

elehnert10x commented 8 months ago

Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.