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  • Script to thousands of exons

    Hi!

    I'm not an expert on informatics so i thought some of you may be able to help me...
    I have a list of about 5000 genes and i want to download only the exons of each of them (maybe through ensembl site). It's too much to do it "by hand" and i really don't have that time.
    Do you have any idea of how could i do it? Any script that could help me with this?

    Thank you in advance for all the attention
    Best regards,
    Sofia

  • #2
    No script should be needed. Use BioMart to do this yourself.

    Go to Ensembl. Click on BioMart link at the top. A new page should open. Going to show an example for human genome. Hopefully genome of your interest is in BioMart.

    1. Choose DB --> Ensembl Genes
    2. Choose Dataset --> Human (as example)
    3. Click on Filters in left column. Many choices open up on right. Choose what you need
    4. Checking Source --> Ensembl for this example
    5. Click on the Attributes in left pane
    6. Select Sequence button in right pane
    7. Expand "Sequences" options by clicking on + sign
    8. Select "Exon sequences" radio button
    9. Expand "Header Information" by clicking on + sign. Select options as needed
    10. Click on the "Count" button at top left corner (e.g. 6460 / 63967 Genes)
    11. Hit "Results" button next to count.
    12. Use "Export results to file" --> "Fasta"
    13. Click on "Go" to download the file (choose unique only if you want that).
    14. You are done!

    Comment


    • #3
      Amazing!

      Thank you SO much!!!

      Comment

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