Adding a Reference Sequence

Click the + Add reference files button under the Reference Files section header and choose Reference sequence from the Library type drop-down list in the Add reference sequence dialog (Figure 1, left). If a cytoband file is already associated with an assembly, Reference sequence will be the only option available in the Add reference sequence dialog and will not appear in a drop-down list (Figure 1, right).

Figure 1. Add reference sequence dialog. If the reference sequence and cytoband files have not been added yet, both options will appear in the Library type drop-down list (left). If one is missing, it will appear as the only option (right). For many model organisms, automatic downloads are available from the Connected Multiomics repository.

If you are using an assembly supported by Connected Multiomics (e.g. human), select Download reference sequence and click Create to get the reference sequence from the repository. Alternatively, select Import reference sequence and click Create to add the reference sequence from another source.

If you are using a custom assembly (e.g. for a non-model organism), the Download reference sequence option will not be available (Figure 2).

Figure 2. For custom assemblies, automatic downloads are not available so the reference sequence has to be imported from another source.

The Import reference sequence option allows you to add a reference sequence from the Partek Flow Server or My Computer (Figure 3). Please choose the option of My Computer.

Figure 3. A reference sequence can be added from My Computer.

You can specify multiple fasta files (e.g. one file per chromosome) and ICM will concatenate them. If a fasta file is imported, a 2bit version of the file will automatically be created and vice-versa. ICM will also accept a range of compressed file formats (gzip, bzip2, zip, tar). If a compressed file is imported, it will automatically be uncompressed and processed.