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Set Parameters

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Set Parameters

1. Open Reference Builder (Instruments) from BaseSpace Sequence Hub as follows.
  1. Select the Apps tab, and then select Reference Builder (Instruments).
  2. From the Version drop-down list, select 1.0.0.
  3. Select Launch Application.
2. To override the default name, enter a preferred name in the Analysis Name field.

The default is the app name with the date and time the session started.

3. To save the output reference genome file to an existing project, select Select Project from the Save Results To field, and then select a project.
4. [Optional ]To save the output reference genome file to a new project, perform the following steps.
  1. From the Save Results To field, select Select Project.
  2. Select New.
  3. Enter a name and an optional description for the new project.
  4. Select Create.
  5. Select the newly created project and then select Select.
5. Select the instrument for which the custom reference genome is intented.

This version of the Reference Builder (Instruments) app supports only the NextSeq 1000 and NextSeq 2000.

6. In the Name field, enter a unique name for the output reference genome file.

This name appears in the Reference Genome dropdown menu when performing run setup in BaseSpace Sequence Hub. It corresponds to the ReferenceGenomeDir value in v2 sample sheets and also the directory on the instrument in which the output reference genome file is saved.

NOTE

The name must be unique for all ReferenceGenomeDir values within the personal or workgroup account or the application will fail.

7. In the Organization field, enter the name of the organization that is associated with the output reference genome file.
8. In the Species field, enter the species for the output reference genome file.
9. In the Source field, enter the source database of the FASTA input file.
10. In the FASTA Input File field, select Select Dataset File(s) and select the FASTA input file.

If the selected FASTA input file contains alt contigs, you must specify a SAM liftover file in the next step or the application will fail.

11. From the SAM Liftover File drop-down list, select the SAM liftover file, if required. Otherwise, leave the selection as None.
  • If you choose to use a custom SAM liftover file, select Select Dataset File(s) from the Custom SAM Liftover File field, and then select the custom SAM liftover file.
12. [Optional ] From the GTF Annotation File field, select Select Dataset File(s), and then select theGTF annotation file.
13. If you choose to use a GTF annotation file, in the GTF Source field, enter the source from where the annotations came.
14. Select Launch Application to build the custom output reference genome file.

When the application finishes, the new custom genome is available for use when performing run set up. To use the new custom reference genome locally, the GZIP file must be saved to a location accessible by control software, eg, a USB drive or a network-accessible drive.