As a user of the Optimus pipeline, I expect functional equivalence for the pipeline with cellranger, or for it to perform better. The latest version of cellranger v3.0 has a mechanism for identifying chimeric reads.
The term Chimera refers to the chimeric molecules that are composed of part of two different reads. Chimera formation is a well documented phenomenon that occurs during PCR amplification. Their overall abundance in scRNA-seq has been estimated to ~5%. Due to the read structure for 3’ assays, chimera formation results in the generation of reads that have a CB and UMI pair incorrectly assigned to a transcript.
Currently available solutions for chimera correction include a proprietary closed source algorithm implemented by cellranger, two algorithms available as part of the Schimera package, and our internal tool being developed in the CellBender package by Mehrtash and the Cellbender team.
AC:
A tool is selected for doing chimeric read correction
Implemented in pipeline, released
Benchmark changes to outputs
Update tests if necessary
Documentation updated
Handoff to Hornet
Ok for reads to be not removed or marked at this point if determined to be chimeras.
As a user of the Optimus pipeline, I expect functional equivalence for the pipeline with cellranger, or for it to perform better. The latest version of cellranger v3.0 has a mechanism for identifying chimeric reads.
The term Chimera refers to the chimeric molecules that are composed of part of two different reads. Chimera formation is a well documented phenomenon that occurs during PCR amplification. Their overall abundance in scRNA-seq has been estimated to ~5%. Due to the read structure for 3’ assays, chimera formation results in the generation of reads that have a CB and UMI pair incorrectly assigned to a transcript.
Currently available solutions for chimera correction include a proprietary closed source algorithm implemented by cellranger, two algorithms available as part of the Schimera package, and our internal tool being developed in the CellBender package by Mehrtash and the Cellbender team.
AC:
Ok for reads to be not removed or marked at this point if determined to be chimeras.
┆Issue is synchronized with this Jira Epic