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

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?

scrna-seq normalization
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updated by Shicheng Guo Shicheng Guo • written by madk00k madk00k

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

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written by fanli.gcb fanli.gcb

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

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written by madk00k madk00k

1 answer

Thanks for reply! I will check these papers for sure

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written by madk00k madk00k

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