I was given two sets of fastq files, one of them is gene expression data and the other one contains the information of the samples that were hashtagged using total seq B antibodies. I was asked to use hashsolo to analyze the data and I am a bit confused about how to do that.
If I use the hashsolo on the fastq files with the hashtagging information then how do I connect that to the gene expression data?
I read in a paper that they used cellranger count and used the hashtags as antibody capture and then input the output matrix which contains both the gene expression and hashtag matrixes in python and used hashsolo. However, when I tried to do that I could not get hashsolo to work because the hashtag information was in the .var column instead of the .obs. For this approach, I used cellranger count with feature barcode data and put the hashtags as antibody capture and I ended up with one matrix.