Question: Can low abundance transcripts be detected?
Answer: Detection of a given transcript depends on (a) the abundance of the transcript in the cell, (b) the sequencing depth per cell, and (c) the mapping quality. Transcripts expressed at very low levels may not be captured and converted into cDNA and therefore will not be detected in the assay. If the sequencing depth isn't sufficient, the transcript may be converted into cDNA but not detected by sequencing (the sequencing saturation metric reported by Cell Ranger can be used to assess this). The transcript sequences must also map uniquely and confidently to the transcriptome. Multimapped or poorly mapped reads will not be used in the Cell Ranger analysis.
Similarly to other RNA sequencing methods, the absence of detection of a transcript does not indicate that the transcript is absent in the cell.
Products: Single Cell 3', VDJ