I have seen several papers where the authors choose to merge assemblies from different samples together to one massive assembly.
Often samples do not even come from the same source.
I understand that people do that to artificially increase sequencing depth and get better resolution, but it feels like that increases the bias towards chimeric MAGs.
Is there any other benefit to this that I dont see?
I think a logical explanation is you want to have a more comprehensive representation of whatever you are working with. Specially true with RNAseq data assemblies. That said, there is certainly the potential for getting chimeric or otherwise non-representative results, if assemblies that should not be merged are merged.
as GenoMax mentions, the origin of the samples matters. In RNA-Seq different tissues express different transcripts, we ought to merge those assemblies to find a fuller view of the transcripts.
I don't understand what you mean about artificially increasing sequencing depth though. When one merges assemblies there is no sequencing depth to go with the merged assembly. Each assembly may have had a different depth.
no no, forgive my confusing writing. Didnt mean to write sequencing depth meant resolution and by resolution I mean more complete transcripts. And yes thanks for your answers, that makes sense especially when you use RNA data.
no no, forgive my confusing writing. Didnt mean to write sequencing depth meant resolution and by resolution I mean more complete transcripts. And yes thanks for your answers, that makes sense especially when you use RNA data.