Comments (2)
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.
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@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"?
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Related Issues (20)
- scipy.stats.mode() function update results in failed reference construction HOT 2
- Deprecation of kallisto pseudo HOT 3
- empty .fa.gz files when running "extract" HOT 1
- arcasHLA customize not working HOT 1
- [reference] Error: dat/IMGTHLA/hla.dat empty or corrupted.
- Frequent reporting of a null allele for 10X data
- Some alles alleles did not be inferred ? HOT 1
- [IndexError] arcasHLA `reference` -- initial set up HOT 13
- Problems running `customize` HOT 2
- Running paired data results in empty fastq HOT 1
- 0 reads mapped to a single HLA gene
- [KeyError] arcasHLA `convert` - using "group" HOT 4
- Donor/Recipient
- TypeError: only integer scalar arrays can be converted to a scalar index HOT 1
- Giving path to reference dataset in genotype command
- arcasHLA reference error with IMGTHLA>3.34.0
- No HLA name file HOT 1
- unable to install arcasHLA in M3 Mac under conda.
- IMGT/HLA version 3.56.0 and onwards provides large files as zip files HOT 1
- pseudoalignments.tsv error HOT 1
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