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Results tagged with scrnaseq
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user 4885
Use this tag for questions related to single-cell RNA-seq.
2
votes
umap and Louvain clustering on normalized data
There is discussion if scaling the data (making the data range for all genes the same) is something you need for single cell data. The argument is that the expression differences between genes themsel …
- 886
5
votes
Accepted
TCR-seq or scRNA-seq
The 3' gene expression protocol will capture TCR and BCR mRNAs but this may not be very helpful to you. As you already mentioned only the 3' end will be sequenced, which are the constant regions. With …
- 886
5
votes
2
answers
584
views
High percentage of poly A sequences in 10X chromium R2 read
I'm currently analyzing two samples of eosinophil cells isolated from mouse lung and the samples are of very different quality.
According to the Cell Ranger summary 56% of the reads can be mapped to t …
- 886
-1
votes
Accepted
High percentage of poly A sequences in 10X chromium R2 read
I actually figured out what was going on some time ago:
The over-represented sequence is the template switching oligo (TSO) that is used for the synthesis of the second strand (the example is for the …
- 886
2
votes
Accepted
Cellranger results have too many cells
The Barcode Rank plot shows very high background in your sample.
The cell estimation from Cell Ranger will look for a sudden drop in the number of UMIs and use this to call cells. In your case, the dr …
- 886
2
votes
Low custom tdtomato gene content
The solution to your problem probably is adding the full mRNA sequence of your transgene to the reference (as also suggested by acrux).
I had a very similar problem recently when tdTomato expression w …
- 886