Which reference to use for normalization

[ninn...@gmail.com]

Hi all,

I have been searching for a while now, but can't seem to find an asnwer, so I wanted to ask here.

I found this on normalization:

http://gemini.readthedocs.io/en/latest/content/preprocessing.html

However, what is the reference? Is it simply a fasta file of all the chromosomes as available at ensembl ftp?

Thanks!

[Aaron Quinlan]

You will want to use the same reference genome (fasta format)  that you used for sequence alignment.

Best,

Aaron