Using both paired and singletons for alignment to identify DEGs

Question

[Doddamani]

Hi All,

I am focusing on identification of DEGs. Can anyone suggest me whether it is good to use both paired and singleton reads for alignment? whether it has any effect on the downstream process?

Thanks

Answer 1

[Devon Ryan]

With or without is fine. Typically there are very few orphaned reads vs. the number of paired-end reads, so I don't think most people bother including the orphaned reads. There are a few tools out that can't handle single-end reads, but for normal DE this isn't an issue.