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Uploading a custom genome

If your genome of interest is not currently available on Basepair, you can create it by uploading both a FASTA file and a GTF or refflat file. We’ll incorporate them automatically into downstream analyses.

Step 1: Under the Samples tab click Add genome​

Add genome button

Step 2: Add the genome name and necessary files​

Give the genome a unique name, preferably including both the assembly and species information.

Add files:

  • Genomic sequence FASTA file
    (typically ends in .fna, .fa, or .fasta and should be gzipped .gz)
  • Gene-annotation GTF or refflat file
    (typically ends in .gtf or contains “refflat” and must be uncompressed)

Be sure the gene-annotation file matches the genome assembly you’re uploading!

Upload genome files

Optional details can be added below under Genome parameters.

Finally, click Add genome at the bottom to begin uploading the files (usually < 10 min):

Add genome dialog

After the upload finishes, an analysis will automatically start in your current project to index the new genome for each aligner (typically ~1 hr):

Indexing in progress
Indexing complete

Once indexing is complete, your custom genome will be available during sample creation under Custom genomes:

Custom genome option

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