Hello! Thanks so much for building this great pipeline. I would like to use your workflow to quantify HLA expression in 10x 3’ single-cell RNA-seq reads. The reads are single-end (since the barcode+UMI make up R1 and the sequence is in R2). We actually don’t need the HLA allele imputation step since we have imputed HLA alleles already. We were wondering what parts of HLApers may need to be adjusted to be able to do this (e.g. single-cell option for kallisto?), or if you happened to have any recommendations for other methods to look at? We looked into scHLAcount but they don’t use the unmapped reads from the bam file so that is less ideal. Thanks so much for any thoughts!
Hello! Thanks so much for building this great pipeline. I would like to use your workflow to quantify HLA expression in 10x 3’ single-cell RNA-seq reads. The reads are single-end (since the barcode+UMI make up R1 and the sequence is in R2). We actually don’t need the HLA allele imputation step since we have imputed HLA alleles already. We were wondering what parts of HLApers may need to be adjusted to be able to do this (e.g. single-cell option for kallisto?), or if you happened to have any recommendations for other methods to look at? We looked into scHLAcount but they don’t use the unmapped reads from the bam file so that is less ideal. Thanks so much for any thoughts!