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pachterlab / kallisto

Near-optimal RNA-Seq quantification
https://pachterlab.github.io/kallisto
BSD 2-Clause "Simplified" License
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allele-specific expression #335

Open afadda1 opened 2 years ago

afadda1 commented 2 years ago

Hi. i have provided the two different alleles in my reference sequence. however, i'm not sure if kallisto can handle this properly. also, what happens in the case of homozygosity? is the tpm reported for each allele is the tpm for the gene (transcripts from the 2 chromosomes)?

Yenaled commented 2 years ago

Yes, kallisto can do allele-specific expression; just put the two transcripts (one for each of the two alleles) in the transcriptome index. You'll get a TPM value for each transcript. If only one allele is expressed (as in the case of homozygosity), the other allele will have a much smaller TPM (its TPM may not necessarily be zero though because the abundances are assigned to the alleles based on a probablistic framework). The gene-level TPM should be obtained by summing the TPMs of all transcripts (including alleles) associated with that gene.

afadda1 commented 2 years ago

thanks a lot for the explanation. very helpful!