Low Fraction of usable antibody reads in CiteSeq
Bioinformatics Asked by gypti on June 12, 2021
we performed a combined gene expression and CiteSeq experiment with the 10x VDJ kit and 20 conjugated antibodies and sequenced on hiseq. I used cellranger to process the sequencing output. The cellranger summary shows overall good values except for a low percentage of “Antibody Reads Usable” and a low fraction of “Antibody Reads in Cells”. How is it possible that so few antibody reads are usable? Does this mean that most antibodies were not bound to the cell surface? 
One Answer
We have also seen a very similar issue and are also investigating why. Possibly of note, I tried forcing the cellranger program to assign a very large number of cells (10x the actual number of cells we had) using the --force cells option. This appeared to increase the % of usable Ab reads and Ab reads per cell metrics, suggesting that these reads may be associated with barcodes that have relatively few UMIs?
Answered by Mike on June 12, 2021
Add your own answers!
Ask a Question
Get help from others!
Recent Answers
- Jon Church on Why fry rice before boiling?
- Joshua Engel on Why fry rice before boiling?
- haakon.io on Why fry rice before boiling?
- Peter Machado on Why fry rice before boiling?
- Lex on Does Google Analytics track 404 page responses as valid page views?
Recent Questions
- How can I transform graph image into a tikzpicture LaTeX code?
- How Do I Get The Ifruit App Off Of Gta 5 / Grand Theft Auto 5
- Iv’e designed a space elevator using a series of lasers. do you know anybody i could submit the designs too that could manufacture the concept and put it to use
- Need help finding a book. Female OP protagonist, magic
- Why is the WWF pending games (“Your turn”) area replaced w/ a column of “Bonus & Reward”gift boxes?