Single-cell RNA-seq normalization with ERCC

kobeho24 · 12-03-2016, 01:24 AM

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

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12-03-2016, 01:24 AM	#1
kobeho24 Member Location: HKUST, Hong Kong Join Date: Apr 2015 Posts: 32	Single-cell RNA-seq normalization with ERCC 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 Last edited by kobeho24; 12-03-2016 at 01:41 AM.