Question: Why am I getting 5' capture of my transcripts on the 3' single-cell assay?
Answer: The 3' assay should capture reads that map back to the 3' ends of the transcripts. If the full-length transcripts are relatively short they will not get fragmented and will carry through the final library. Occasionally, we also see reads that map to regions that are outside the 3' portion of a gene and these regions map back to 5' or intergenic regions as they contain a polyA stretch; which the polyT-Gel Bead oligos can bind to. The BAM file can show whether this 5' read has a stretch of A nucleotides.
Products: Single Cell Gene Expression