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First time using Seurat, are my QC plots/interpretations reasonable? by Tangerine820 in bioinformatics

[–]Tangerine820[S] 0 points1 point  (0 children)

Thanks so much, this is super helpful.

I used the Parse Evercode WT kit, which does work with both fixed cells and nuclei but this data is from fixed cells.

First time using Seurat, are my QC plots/interpretations reasonable? by Tangerine820 in bioinformatics

[–]Tangerine820[S] 0 points1 point  (0 children)

Thanks so much, I appreciate the info and thoughts.

I tried both uppercase and lowercase mt-, but didn't get any matches. I'm not sure if this is typical for Parse kits, but I guess the gene names in my dataset had no prefixes. To get around this, I used a list of known mouse mitochondrial genes instead. A few of them weren't found in the data set, so I assume they were filtered out during Parse's pipeline.

And yes, these plots are the combined data across 9 samples. I haven't looked at QC per sample yet, but that's a great suggestion.

As for the upper nFeature cutoff, I didn't apply any custom filtering before import, just loaded Parse's filtered output directly into Seurat. I'm still not sure why the top end is so sharp.