Entering edit mode
6.1 years ago
rob.costa1234
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310
I am planning to do single cell RNA-seq with 10X genomic platform. I was wondering if there are any rules to select how many cells I should use and how many reads per cell will be optimal. I have looked into 10x web page (https://support.10xgenomics.com/single-cell-gene-expression/sequencing/doc/specifications-sequencing-requirements-for-single-cell-3) and googled this. There are lots of variations in different publications fro the number of cells sequenced and number of reads per cell. Any suggestion
Have you considered contacting 10x support directly? They should have this information.
BTW: Page you linked clearly says this
there is lot of variation in reads per cell, some go upto 100K to several millions of reads. That is the major cause of confusion. I will write to 10X
You should also add information here about what kind of cells you are looking to sequence and for what organism (to get an idea of genome/transcriptome complexity/size).
You have asked a number of questions here but have not validated answers for many of them. Please consider doing so. This is a way to acknowledge help you receive and to provide some assurance for future visitors that the information/solution provided was useful in solving the stated problem.
You might want to look at http://10xqc.com/