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