Question: Should I adjust the targeted sequencing depth if I know the percent of T or B cells in my heterogenous sample?
Answer: If sequencing V(D)J-enriched libraries, yes. The sequencing depth recommendations provided in the User Guide are for enriched T- or B-cell samples. Only Ig or TCR expressing cells will be detected in enriched libraries, so if the B or T cell fraction is known, adjust the sequencing depth accordingly. If this information is not available, sequence according to the recommendation for the total targeted cell load.
For 5' gene expression libraries, do not adjust the sequencing depth by the expected B or T cell fraction. The mRNA transcripts in all cells will be profiled.