Multi Alignment - How to deal with uncertainty?

Question

[andrebolerbarros]

Hi everyone,

I have samples which align with two different genomes with a great degree of similarity. Is there any way to handle/correct/take into consideration reads that align to two genomes?

Currently, I'm working on DEG using R and DESeq2.

Thanks in advance

[GenoMax]

Sounds like these are xenograft (type) datasets, if not for mouse/human. Considerations like this can still apply. An example paper :
https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-019-0551-2
https://www.nature.com/articles/s41467-021-25177-3

[andrebolerbarros]

That's a very good suggestion, hadn't thought about it. Thanks!