Genome for mouse Chip-seq analysis

Question

[luckysardar171]

Hello, I am working on chip-seq analysis , data is from mouse cells, which genome reference to select from the database latest mm10 genome and GTF. Is ensemble reference genome will be fine, because in encode project reference file has a name mm10_no_alt_analysis_ set_encode. don't know what does it mean any suggestions.

please provide me the link to download the genome.

Thank you

Answer 1

[ATpoint]

https://www.gencodegenes.org/mouse/

I would use Genome sequence, primary assembly (GRCm38) as genome reference and the GTF called Comprehensive gene annotation. That is basically the common reference for mouse these days. Ensembl uses GENCODE as well.

[luckysardar171]

Thank you for the replay