Question: Mouse mm10 genome
gravatar for VY
2.6 years ago by
VY120 wrote:

Kind of a naive question, but is the mm10 genome on galaxy the same as GRCm38.ERCC mouse genome?

genome mm10 mapping • 4.0k views
ADD COMMENTlink modified 7 days ago by • written 2.6 years ago by VY120
gravatar for Jennifer Hillman Jackson
2.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The mouse mm10 genome indexed at Galaxy Main is sourced from UCSC based off of NCBI's GRCm38. These are the credits:

While GRCm38 from NCBI is technically the same build (in terms of sequence content), the sequence identifiers will differ between the original at NCBI and what UCSC produces. Then ERCC RNA data is an extra layer of annotation added to base genomes available at certain sources (GEO and Ensembl host these, I believe, and perhaps others). The source mm10 from UCSC used at Galaxy Main does not include this content.

If you wish to use a different genome version for mouse than what is available at Galaxy Main, a local/cloud Galaxy can be used with a genome added with a Data Manager (from any source) or you can try using the Custom Genome feature at Galaxy Main - just be aware that using such a large genome as a custom genome may create jobs that run out of memory.

It is important to use the same exact reference genome version for all steps in an analysis or unexpected results are to be expected.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.6 years ago by Jennifer Hillman Jackson25k

I didnot find mm10 Fasta format in data library. Could you specify, How can I add ref.genomes to the history panel (similar to adding .gtf files from galaxy library)?

ADD REPLYlink written 12 months ago by bioadept0
gravatar for
7 days ago by wrote:

And one should take into account, that NCBI coordinates are 1-based while UCSC's are 0-based!

ADD COMMENTlink written 7 days ago by

To be clear, in practical terms, the start coordinate format (0-based or 1-based) is dependent on the datatype of the dataset/file. This is independent of the underlying version of the reference genome.


ADD REPLYlink written 7 days ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour