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i5k Workspace@NAL
U.S. Department of Agriculture
  1. I5k Workspace data management policy
  2. Accepted data types: Mapped files

Accepted data types: Mapped files

  1. Accepted file formats (these largely depend on what the JBrowse genome browser accepts)

    1. Bam (http://samtools.github.io/hts-specs/SAMv1.pdf)

    2. Bigwig (https://genome.ucsc.edu/goldenpath/help/bigWig.html)

    3. Vcf (https://github.com/samtools/hts-specs)

    4. Gff3 (https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md)

    5. bed (https://genome.ucsc.edu/FAQ/FAQformat.html#format1)

  2. Data type examples (anything is possible if you can map it and your community can benefit)

    1. RNA-Seq

    2. DNA-Seq

    3. Variant Data

  3. Constraints

    1. All mapped files must be submitted to us on the coordinate system of the assembly that we host (e.g. GenBank). You can find the assembly in our data downloads section, or contact us.

    2. If you did not use this assembly, there may be problems displaying the mapped data in the JBrowse genome browser. In this case, we may provide guidance or assistance on how to transfer coordinates or re-map your annotations.

  4. File processing services

    1. We routinely convert bam files submitted to us to bigwig format for easier display in the genome browser, unless requested otherwise. Generally, we use this pipeline for conversion.

    2. We can also reduce bam file coverage for you, on request. We may also recommend this to you if we think your bam file is too dense to display well in the genome browser.