Mean Reads Per Cell (SCrna Seq)

Question

[CuriousSeq]

What are ‘reads’ in mean reads per cell? What are 'reads' in mean reads per cell?

[ATpoint]

Before you start analyzing a rather complicated assay like scRNA-seq, I strongly recommend to spend some quality time on getting a background in sequencing, simply to know what you are analyzing, and being able to understand the vocabulary.

Answer 1

[GenoMax]

If this question is about 10x cellranger data then details can be found at this link.

Mean Reads per Cell = The total number of sequenced reads divided by the estimated number of cells.

[CuriousSeq]

How does one increase the total number of sequenced reads

[GenoMax]

By sequencing library pool again on a new flowcell.

[CuriousSeq]

Thank you. With the Illumina Platform (HiSeq 2500), is there an average amount of reads attained per flowcell

[GenoMax]

You can find the published specifications here. Keep in mind the numbers are for normal genomic sequence. Sequencing facilities may or may not guarantee the number of reads mentioned. Ultimate yield will depend on the quality of library being sequenced.

Answer 2

[Devon Ryan]

Reads are the things produced by the sequencer.