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Single Cell

Can we use TranSeq to analyze single cell data?

We used this protocol to prepare libraries for low number of cells (~1-10 cells). Is this pipeline adequate for such data?




Barak Markus
1 Answer


In principle you can use this pipeline to analyze such data. The pipeline will run DESEQ for both the read counts and the UMI counts. However, we did not optimize this pipeline for data. In particular there should be more filtering options before counting UMI’s/reads and some specific QC measures that we did not implement. In addition we are not sure that DESEQ is the right statistical framework for single cell analysis.

If you have less than ~1000 cells in your samples we suggest that you contact us.


Barak Markus

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