I am trying to align and merge different samples from NCBI. I end up having correlation problem with these sample. The picture below shows an heatmap of the R² by doing a linear regression between 2 samples' count matrices.
Samples A, B and C are from the same project and sample D from another. A, B and C are sequenced using the 10X Genomics for Single Cell V(D)J + 5' Gene Expression, and Chromium Next GEM Single Cell 3ʹ v3.1 for sample D.
All samples have been recovered from NCBI using
fastq-dump — internaly threaded to be more efficient — and aligned using
cellranger with the default human genome given by 10x.
QC shows some GC content small shifts along side some huge duplication level — even for scRNA-seq.
Am I missing something important when it comes to merge datasets?
Thank you very much