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RabadanLab / arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq
GNU General Public License v3.0
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Can I use arcasHLA for cancer scRNA-seq data? #49

Closed levinhein closed 3 years ago

levinhein commented 3 years ago

Can I use arcasHLA for cancer scRNA-seq data?

IoanFilip2 commented 3 years ago

Thank you for your interest in your tool. At the moment, arcasHLA cannot be used directly for calling HLA alleles in single cells. However, you may use arcasHLA to genotype the tissue of origin by simply processing the single-cell bam file as if it were a single-end bulk sample (by ignoring the cell barcode mate). The pipeline will produce highly accurate genotyping as it normally does for single-end bulk samples. We are in the process of developing a cell-specific approach based on arcasHLA. In the meantime, please let us know if you have follow-up questions.

gt7901b commented 3 years ago

@IoanFilip2 I have samples with both bulk and single-cell RNA-seq. I ran arcasHLA on single cells as you suggested above and the results match bulk. Thanks for developing such a nice tool.
what do you mean "a cell-specific approach based on arcasHLA"?