To give you some context:
We have an experimental setting with 2 samples, where GEX (gene expression) and ADT (antibody labelling) libraries are generated from the same sample. So, in total, 4 samples are generated corresponding to 2 pairs of paired GEX-ADT samples.
Specifically following the directions from previous thread https://support.bioconductor.org/p/120645/, all 4 samples were multiplexed together in the same sequencing run, in order to be able to correct for index hopping afterwards. Cellranger processing had to be done separately for GEX and ADT samples, as the special “Feature Barcoding Analysis” was required to be able to process the latter.
However, when we proceeded to run swappedDrops() on the resulting molecule information files (4 in total, 1 per sample), this was not possible due to error “gene information differs between samples”. And indeed, the resulting set of features is different for GEX and ADT, namely genes and antibody tags, respectively. Nonetheless, this came as a surprise for us, as the answers and discussions from the mentioned thread mislead us to believe that performing index hopping removal via swappedDrops() was possible for different libraries, just as long as they were multiplexed together.
So our questions would be:
- Is this not the case? Can't we use swappedDrops() at the same time on different libraries that were multiplexed together?
- If not, how is swappedDrops() supposed to be used when one has an experimental design such us ours? The specific setting was chosen to begin with in order to comply with swappedDrops() requirements..
Thank you in advance.