Reply
Highlighted

minimal reads per cell required to determine if a sample library will give quality data

Posted By: NG, on Nov 16, 2017 at 2:26 AM

Hello,

 

Not all samples we process are of high quality. Thus, we would like to minimally sequence each sample first to see if we can get good data, before we decide to invest more money and to "deep sequence" the samples.

 

Can you recommend a minimal number of sequencing reads per cell (shallow test-sequencing) for a given cell type (e.g. PBMCs) that would be sufficient for a quick quality control of the samples before moving on with a deep and costly sequencing run?

 

Thanks for your help

NG

 

2 Replies

Re: minimal reads per cell required to determine if a sample library will give quality data

Posted By: eieimin, on Nov 16, 2017 at 9:27 AM

Dear NG,

 

Yes, you can run a QC check on MiSeq with shallow sequencing depth, before "actual" sequencing run, if you have enough materials.

 

You do not need to sequence deep for MiSeq-QC check. For example, if you have 20,000 cells total (4 10x Chromium Single Cel libraries; each with 5000 cells), the MiSeq kit with 25M reads would generate 1250 reads/cell, which is fine for a quality check run.

Please let me know if you need additional information, and for more details please visit https://support.10xgenomics.com/single-cell-gene-expression/sequencing/doc/specifications-sequencing...

 

Best,

Ei Ei

 

Re: minimal reads per cell required to determine if a sample library will give quality data

Posted By: EricBindels, on Jul 23, 2018 at 9:36 AM

which miseq flowcell?

MiSeq Reagent Kit v3 (150-cycle)???