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
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asyndeton17 •
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.
That seems reasonable. Will I be able to keep track of which condition cells came from within the matrix? If so, how?
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.
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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.
Yes, there are many cells for each condition, but I want to plot both conditions onto one plot (probably a PCA plot).