Question: Combining Conditions in scRNA-seq (Drop-seq) for Analysis
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gravatar for asyndeton17
22 months ago by
asyndeton1720
asyndeton1720 wrote:

Hi,

I recently ran a Drop-seq experiment and got my demultiplexed data back for two different conditions. When should I combine the two files together? I began with two queryname-sorted BAM files. Should I merge the files after alignment, right before alignment, or after I extract the matrix for each condition?

Thanks

rna-seq drop-seq scrna-seq • 1.0k views
ADD COMMENTlink modified 22 months ago by Devon Ryan90k • written 22 months ago by asyndeton1720

What's the goal? I assume you have multiple cells for each condition and are able to get counts for each. Normally you'll be using a matrix of that.

ADD REPLYlink written 22 months ago by Devon Ryan90k

Yes, there are many cells for each condition, but I want to plot both conditions onto one plot (probably a PCA plot).

ADD REPLYlink written 22 months ago by asyndeton1720
1
gravatar for Devon Ryan
22 months ago by
Devon Ryan90k
Freiburg, Germany
Devon Ryan90k wrote:

For PCA (or tSNE, which is likely what you'll end up doing), you'll need a matrix with all of the cells for both conditions. Don't "merge" things in any other way.

ADD COMMENTlink written 22 months ago by Devon Ryan90k

That seems reasonable. Will I be able to keep track of which condition cells came from within the matrix? If so, how?

ADD REPLYlink modified 22 months ago • written 22 months ago by asyndeton1720

Normally you just cbind() them and will know beforehand how many come from each cell type, so yes. But the responsibility for doing that is on you.

ADD REPLYlink written 22 months ago by Devon Ryan90k
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