I am having an issue with my single cell data set. This alert was shown after I requested additional reads per cell to be incorporated with the initial data we received.
We have previously performed single cell on this tissue so I am pretty certain that the issue is not due to trying to identify rare transcripts. We sent this data for sequencing to further test a hypothesis that a specific cell population is a major "expresser" of a gene of interest. We have shown this in multiple ways so far. I am seeing trends in the data that is in line with what we have previously found but the cell count is so low that my violin plots do not give a violin and I have sparse dots on the umap. See below.
the goal is to show that genes 1,2 and 3 are expressed in the same cluster, cluster 0. I am at my wits end with trying to represent this data. We have tried doing deeper sequencing to no avail. Does anyone have any idea is there is a way to represent this data as is in a way that makes sense. I don't think violin plots or umap plots will be useful here. Like I said, this is not our only piece of data so we are pretty confident that the finding is real.
Also, on the sequencing/10X side, is there anyway to improve data quality given this type of error? Note that we did not observe this error (picture 1) on the first round of sequencing.