For most applications (except de novo sequencing), you will need reference data in the form of a reference genome sequence, annotations, known variants etc. There are three basic ways of obtaining reference data tracks:
- Use the integrated tool for downloading reference genomes as tracks.
- Import tracks from files (learn more in Import tracks from file).
- Convert sequences with annotations to tracks (learn more in Converting data to tracks and back). Sequences can come from a variety of sources:
- Standard Import ()
- The standard import accepts common data formats like fasta, genbank etc. (learn more in Bioinformatic data formats)
- Downloading from NCBI
- The integrated tool for searching and downloading data from NCBI (learn more in GenBank search).
- Contigs created from de novo assembly.
- Contig sequences from de novo assembly can be considered a reference genome for e.g. subsequent resequencing analysis applications.
- Use the special plugins that integrate with Biobase's Genome Trax (learn more at http://www.clcbio.com/clc-plugin/biobase-genome-trax-download/).
Please note that tracks are not yet supported with the transcriptomics tools of CLC Genomics Workbench
. This means you have to provide standard sequences (downloading from NCBI or importing files).