Uploading a custom genome

If your genome-of-interest is not currently available on our platform, you can create it by uploading both

FASTA and GTF/refflat files to Basepair. We will then handle their incorporation into downstream analyses.

Step 1: Under the "Samples" tab click "Add genome"

Step 2: Add the genome name and necessary files

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

Add files:

    - genomic sequence FASTA file

        (typically ending in ".fna", ".fa", or ".fasta" and should be gzipped ".gz")

    - gene annotation GTF or refflat file

        (typically ending in ".gtf" or containing "refflat" and must be uncompressed)

*be sure that your gene annotation file was built for the genome assembly you are uploading!

Optional information can be added further below under "Genome parameters"

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

After the upload has completed, an analysis will automatically start in your current project.

This analysis will index your new genome for each aligner used by Basepair (typically ~1hr):

Once this has all completed, your custom genome will now be available during sample creation under "Custom" genomes for use in data analysis: