Cnv-seq On Mouse Data

[arcolombo698]

Hi, I am interested in using CNV-seq on mm10, however, when I use the command line the genome for mouse is not avail... is this CNV-seq software not useful for mm10 ref genomes?


--genome = (human, chicken, chrom1, autosome, sex, chromX, chromY)
(higher priority than --genome-size)

[arcolombo698]

What I did was under --genome command, I included the same fasta file used for alignment of the mouse genome.

However, I am not sure this is allowed. I know for RDxplorer, the manual says that it is for HUMAN ONLY.

Has anyone used CNV-seq on mm10 reference genome?

[vbajic]

is this CNV-seq software not useful for mm10 ref genomes?
(higher priority than --genome-size)

It is useful for mm10. In the manual it is written that either --genome or --genome-size option must be specified. So if you know genome size you can set up that one. However, I am not sure if that would work if you are using the whole genome with all chromosomes (since you are entering in --genome-size just one number and program needs to know size of each chromosome). I am working just on one chromosome and I set up --genome-size. I didn't upload any fasta file.