Hello! I've gotten all of SCALPEL to successfully run on my files. However, my output DIU_table.csv says "Provide more condition with levels > 1 for differential isoform usage analysis."
I looked at the src code analysis_samples.R and saw that the expected format is a three-column TSV with each column corresponding to "orig.ident", "Barcodes", "Clusters".
My interpretation of this led me to provide an input file that had the first column as my mouse's sample ID, the second column as the barcode, and the third as the celltype ID (labeled with celltype and condition) I've assigned to the cell. My end goal is to be able to compare the isoform usage between the cell types. I don't really care about the mouse sample ID (I have 8 biorep samples for my two conditions).
I would appreciate any direction on correcting my input file!
Hello! I've gotten all of SCALPEL to successfully run on my files. However, my output DIU_table.csv says "Provide more condition with levels > 1 for differential isoform usage analysis."
I looked at the src code analysis_samples.R and saw that the expected format is a three-column TSV with each column corresponding to "orig.ident", "Barcodes", "Clusters".
My interpretation of this led me to provide an input file that had the first column as my mouse's sample ID, the second column as the barcode, and the third as the celltype ID (labeled with celltype and condition) I've assigned to the cell. My end goal is to be able to compare the isoform usage between the cell types. I don't really care about the mouse sample ID (I have 8 biorep samples for my two conditions).
I would appreciate any direction on correcting my input file!