Gene id conversion: Difference between revisions

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(New page: * [http://hum-molgen.org/NewsGen/08-2009/000020.html List of tools and comparison] * With biomart http://www.biomart.org (the best if your source ids are in Ensembl format), click on: ## m...)
 
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* [http://hum-molgen.org/NewsGen/08-2009/000020.html List of tools and comparison]
* [http://hum-molgen.org/NewsGen/08-2009/000020.html List of some external tools and comparison]
* With biomart http://www.biomart.org (the best if your source ids are in Ensembl format), click on:
** David and Matchminer were the best ones when compared with 100 random identifiers
 
* With biomart http://www.biomart.org (probably the best if your source ids are from Ensembl), click on:
## martview (top-right of screen)
## martview (top-right of screen)
## ensembl56 genes
## ensembl56 genes
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## check "HGNC symbol" (or "HGNC automatic gene name" if not human)
## check "HGNC symbol" (or "HGNC automatic gene name" if not human)
## "results"
## "results"
* With UCSC tools: [https://lists.soe.ucsc.edu/pipermail/genome/2009-March/018423.html|this thread] (best option if your source IDs are UCSC knownGenes or if you prefer the table browser to biomart)

Revision as of 17:02, 5 December 2009

    1. martview (top-right of screen)
    2. ensembl56 genes
    3. (select your species)
    4. "filters"
    5. "gene"
    6. paste your ids into "id list limit"
    7. "attributes"
    8. "GENE"
    9. uncheck "ensembl transcript id"
    10. uncheck "ensembl gene id" if you want to get rid of it
    11. "EXTERNAL"
    12. check "HGNC symbol" (or "HGNC automatic gene name" if not human)
    13. "results"
  • With UCSC tools: thread (best option if your source IDs are UCSC knownGenes or if you prefer the table browser to biomart)
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