Single cell RNA-seq with ERCC spike-ins: appropriate normalization methods for cell types investigation
1
0
Entering edit mode
5.0 years ago
madk00k ▴ 350

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 • 3.9k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
2
0
Entering edit mode

Thanks for reply! I will check these papers for sure

ADD REPLY

Login before adding your answer.

Traffic: 1394 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6