Use the UCSC Genome Browser to create a BED file with padded exons

Use the following example of creating a BED file with padded exons using the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables).

  1. In the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables), make the following selections from the dropdown lists.

    Field

    Selection

    assembly

    Feb.2009 (GRCh37/hg19)

    group

    Genes and Gene Predictions

    track

    NCBI RefSeq

    table

    UCSC RefSeq (refGene)

    output format

    BED - browser extensible data

  2. In identifiers (names/accessions) section, click either paste list or upload list.

    Depending on your selection, Paste in Identifiers or Upload Identifiers screen opens.

  3. Either upload a text file by clicking Choose File, or paste the list into the provided field, then click submit.
  4. Click get output.

    The Output refGene as BED screen opens.

  5. In the Create one BED record per:, make one of the following selections.

    • Add upstream or downstream base padding.

    • Add bases at each end of the exons.

    • Include 5' or 3' UTR Exons, or only coding exons

  6. Click get BED.

Upload the BED-formatted file to Ion AmpliSeq™ Designer.

Related Topics
Parent topic: Create a BED file from a list of variants