How to improve alignment of scRNA-seq data in using CellRanger

Question

[otieno43]

How can one improve scRNA-seq read alignment in Cell Ranger. I have read in several papers that one can incorporate 3' or 5' UTRs during alignment process. My script looks something like this (below) and it works perfectly well (with good coverage), but just want to enhance coverage:

## To create custom references, by indexing with cellranger mkref
cellranger mkref --genome=Trips_index --fasta=/gpfs/ysm/project/Genomes/Trips_Genome.fasta --genes=/gpfs/ysm/project/Genomes/Trips.gtf

## To generate single cell feature counts for a single library
cellranger count --id=Trips_index_out \
                 --transcriptome=/gpfs/ysm/project/T_congoSc/Trips_index \
                 --fastqs=/gpfs/ysm/from_louise/Trips_scRNA-seq \
                 --sample=Trips

Any one who knows how to do this help.

Erick

[GenoMax]

See the section on adding genes: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references and https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr#marker

[otieno43]

I developed the above script from the information on the links you have paced here (link). I can not just get how to do it.

[dsull]

The original poster is correct: alignment can be improved (and how to best do so is an active area of research which is why it's not in the CellRanger workflow).

https://www.biorxiv.org/content/10.1101/2022.04.26.489449v1