search

galelab / scPathoQuant

single cell pathogen alignment and quantification tool
BSD 3-Clause "New" or "Revised" License
7 stars 1 forks source link

custom reference with the viral sequence added to human reference #5

Open sm2695 opened 3 weeks ago

sm2695 commented 3 weeks ago

Hi,

Thank you for developing a great tool! Does the tool only take unaligned reads from cellranger's output?

I ran cellranger count on my files with a custom reference containing the human reference genome and the viral genome added to it as a single exon. This also results in viral transcripts being 'aligned' to this reference. Does it make sense to run scpathoquant on such output files?

Thanks in advance!

lwhitmore commented 2 weeks ago

Hi, It does not make sense to run scPathoQuant on that output if the viral genome has already been added to the human reference genome. scPathoQuant would not find any viral reads as they have already been aligned in the first analysis. Thanks for your question and let me know if you have others!