Question: Using UCSC Genome Browser with results from NCBI or Ensembl assemblies
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gravatar for colin.kern
3 months ago by
colin.kern150
United States
colin.kern150 wrote:

If I want to display some data on the UCSC genome browser, but have done the analysis with the Ensembl or NCBI assemblies and annotations, do I need to manually write scripts to replace all the chromosome IDs with the UCSC genome browser ones? It seems like this would be a very common situation that has an existing solution.

Alternatively, I could do my analyses from now on using the UCSC assembly and annotation files, but that seems to have some issues. The annotation is only distributed as a SQL database. I have looked at using the Table Browser in UCSC to get a GTF file, which is what most tools use, but the GTF files I can get have a lot of missing information. They only contain stop_codon, start_codon, exon, and CDS elements. Can I get it to have transcript and gene entries also? It also only gives the gene and transcript IDs, whereas the GTF files you can get from Ensembl or NCBI have a lot of useful information such as gene symbol and biotype.

I think I might be missing something because it seems like I'm having to jump through a lot of hoops for something that I suspect a huge number of people have dealt with before.

ucsc browser ensembl ncbi • 261 views
ADD COMMENTlink modified 3 months ago by Emily_Ensembl14k • written 3 months ago by colin.kern150
1
gravatar for Pierre Lindenbaum
3 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum106k wrote:

do I need to manually write scripts to replace all the chromosome IDs with the UCSC genome browser ones?

yes and Devon's work wil help you : https://github.com/dpryan79/ChromosomeMappings

it seems like I'm having to jump through a lot of hoops

sed is your friend

ADD COMMENTlink written 3 months ago by Pierre Lindenbaum106k

Thanks. Do you know what resources were used to make those mappings? I work with farm animal species and none of them are on that Github.

ADD REPLYlink written 3 months ago by colin.kern150
1
gravatar for Emily_Ensembl
3 months ago by
Emily_Ensembl14k
EMBL-EBI
Emily_Ensembl14k wrote:

Or you could display the data in Ensembl.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Emily_Ensembl14k
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