Could you please add the human mitochondrial genome in the database list? Thank you.
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Hello @Mayur_Doke
The genome is small enough to use as a custom reference genome/build.
FAQs:
- Preparing and using a Custom Reference Genome or Build
- Mismatched Chromosome identifiers (and how to avoid them)
That said, the EU administrators may consider adding it as a distinct reference genome with tools. ping @bjoern.gruening @wm75
There are two versions for GRCh38’s mitochondrial assembly in recent use – which do you want? A UCSC identifier (hg38/GRCh38, “chrM”, Link )? Or Ensembl/NCBI identifier (GRCh38, “MT” or NC_012920.1)?
What annotation (if any) and external browser(s) you plan to use will matter for this choice unless you plan on managing the chromosome identifier during your analysis. The FAQs above help to explain.
- https://www.ncbi.nlm.nih.gov/genome?term=human[orgn]
- http://hgdownload.soe.ucsc.edu/downloads.html#human
Thanks!
Thank you jennaj for your reply. I would like to use Ensembl/NCBI identifier (GRCh38, “MT” or NC_012920.1). Thank you
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Ok, two choices:
-
Load that accession up now from NCBI to Galaxy and use it as a custom genome + build. Be sure to follow the FAQ I linked above –
fastadescription line content will be an issue from this data provider and there is a simple tool that will remove it (NormalizeFasta). -
Wait for the EU team to reply. It may not be until Monday (at the earliest) for a reply, and longer for the actual addition + indexing, plus they may still suggest that you use a custom genome/build.
Best!
@jennaj what is your take here? Do we want to offer this genome on usegalaxy.*?
I’m happy to install it.
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