Single-cell RNA-seq normalization with ERCC for isoform analysis

Question

[garyhokawai]

Hi everyone, Does anyone have any recommendation on the single-cell rna-seq data normalization methods? I would like to do normalization across a mix population of cells, in particular, transcript-level analysis is demanded. I know there are a whole bunch of methods doing well on gene-level, just wonder how can we do the similar thing on isoform-level with ERCC as spike-ins.

BTW, I intended to use alighment-free quantification programs such as kallisto or salmon, since I have a hugh dataset and they are much faster and require less computational resources.

Thanks in advance!

Wish you all a merry Christmas and a happy new year

Gary

Answer 1

[Mike]

Hope this post would be helpful ...

Single Cell RNAseq data analysis protocol