hicBuildMatrix not working.
I mapped my reads to a reference genome I uploaded to galaxy, using bowtie2. to obtain a .bam file. I want to run hicBuildMatrix but it is requesting for me to specify genome to be built. the options available doesn’t include my genome which is simulium neavei. How do I proceed?

1 Like

Hi @Millicen

If I understand what you are doing (and please correct me if wrong), you can create a custom database dbkey/database from your custom reference genome fasta. That database can be assigned to datasets.

For the how-to, please see → FAQ: How to use Custom Reference Genomes?FAQ: Adding a custom database/build (dbkey)

Custom database dbkey’s will show up in your account’s database listings in a few places:

  1. Upload
  2. DatasetPencil iconAttributes tab → Database/Build pull-down menu
  3. Importantly, NOT on tool forms directly. Select the custom fasta from the history instead, and the tool will index the genome for that specific tool during runtime as a pre-processing step.

Please let us know if this was enough or not, thanks!