Thanks a lot for developing this great tool.
We want to merge biological replicas using Cellranger aggr after using SoupX(). So far, we have performed the Cellranger count pipeline for each of our biological replicates, obtaining a count matrix (filtered_feature_bc_matrix) for each replicate. Then, we “corrected” the filtered_feature_bc_matrix of each replicate with SoupX(). Now we want to merge/normalize the biological replicas and obtain a new .cloupe file using Cellranger aggr. However, Cellranger aggr needs the molecule_info.h5 file from Cellranger count’s output, and not the corrected filtered_feature_bc_matrix outputted by SoupX(). I was wondering, is there a way to introduce the newly corrected SoupX() matrix as input for Cellranger aggr?
Thanks you very much for your time and help.
Thanks a lot for developing this great tool.
We want to merge biological replicas using
Cellranger aggrafter using SoupX(). So far, we have performed theCellranger countpipeline for each of our biological replicates, obtaining a count matrix (filtered_feature_bc_matrix) for each replicate. Then, we “corrected” the filtered_feature_bc_matrix of each replicate with SoupX(). Now we want to merge/normalize the biological replicas and obtain a new .cloupe file usingCellranger aggr. However,Cellranger aggrneeds the molecule_info.h5 file fromCellranger count’s output, and not the corrected filtered_feature_bc_matrix outputted by SoupX(). I was wondering, is there a way to introduce the newly corrected SoupX() matrix as input forCellranger aggr? Thanks you very much for your time and help.Gregor