The GEX data from a multiome run can be treated almost identically to that of the GEX samples through cell-seek. The only differences are the need to start with an h5 file from cellranger and to change the initial loading commands to extract just the GEX data. I have adapted the initial script seuratSampleQC.R to account for these changes and uploaded the file here.
My request would be to incorporate the seurat QC and integration steps into the multiome.smk script so that all the seurat steps can run on this GEX data.
This isn't ideal as cell filtering should be done on both the GEX and ATAC data before merging/integration, but since multiome is still problematic, this would be useful to better assess the quality of the GEX side of the multiome samples to see how much of it might still be useful.
seuratSampleQC_multiomeGEX.R.txt
The GEX data from a multiome run can be treated almost identically to that of the GEX samples through cell-seek. The only differences are the need to start with an h5 file from cellranger and to change the initial loading commands to extract just the GEX data. I have adapted the initial script seuratSampleQC.R to account for these changes and uploaded the file here.
My request would be to incorporate the seurat QC and integration steps into the multiome.smk script so that all the seurat steps can run on this GEX data.
This isn't ideal as cell filtering should be done on both the GEX and ATAC data before merging/integration, but since multiome is still problematic, this would be useful to better assess the quality of the GEX side of the multiome samples to see how much of it might still be useful.
seuratSampleQC_multiomeGEX.R.txt