I (and collaborators) recently performed a patch-seq experiment... That is, we did patch-clamp recording of neuronal firing, then aspirated the contents of recorded cells, and made RNA seq compatible libraries.
Data look alright - certainly there is a lot of PCR duplication. Probably a combined effect of too many PCR cycles and no UMIs in the kit we used.
To analyze, I did a STAR -> deduplicate -> htseq-count -> DESeq2 pipeline. I think I am getting meaningful results and cells that are expected to be similar cluster together.
But I have an odd MA plot that is giving me some pause:
The low expression transcripts are DRAMATICALLY skewed toward one group. I am thinking that this must be an artifact. In my downstream analyses, I have filtered based on a minimum of normalized counts, but I am wondering if anyone has encountered an odd graph like this and how you have dealt with it? Should I filter raw reads before performing DESeq? Thanks very much in advance!