Single cell RNA-seq with ERCC spike-ins: appropriate normalization methods for cell types investigation

Question

[madk00k]

I am working on scRNA-seq data generated using ERCC spike-in. Main goal is to investigate the cell types and perform special clustering. I have only have access to the formed fastq files without spikes. Each Fastq file belongs to a certain cell. My question is the following: is the FPKM normalization enough for such analysis? If not, what kind of normalization should be performed to distinguish the cell types correctly?

[fanli.gcb]

What's the point of including ERCC spike-ins if you don't have access to them...?

[madk00k]

Actually the spike-ins are there. I did not perform initially the alignment to ERCC references, only to normal reference, now this is fixed.

Answer 1

[Shicheng Guo]

Four papers you need to read and then you will get the answer by yourself.

http://nar.oxfordjournals.org/content/early/2014/07/22/nar.gku555.full

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902584/

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0805-z

http://www.hubrecht.eu/wp-content/uploads/2015/11/CELL2015.pdf

[madk00k]

Thanks for reply! I will check these papers for sure