Applied Biosystems SOLiD™ 4 System SETS Software User Guide ...

Applied Biosystems SOLiD 4 System SETS Software User Guide
Chapter 2 Prepare Run Settings
Load a Reference Sequence 2
3. Click Browse, then select the appropriate fasta file for your
reference sequence.
4. Enter a name for the selected file and click Submit.
The reference genome name that you enter in step 4 appears in
the Secondary Analysis Settings window in the drop-down list
of reference genome.
IMPORTANT! After uploading the genome, the SETS Software
validates the reference. The validation may take several
minutes, during which the genome is not available. If validation
fails, the new genome is not available in the drop-down list in
the Secondary Analysis Settings and an error log is displayed in
the homepage (under Error Messages).
To upload reference genome files larger than 2GB
Reference genome files larger than 2GB cannot be uploaded through
the SETS Software due to the limitations set by browsers. To upload
reference genomes larger than 2GB:
1. Use an FTP tool to first place the file inside the home directory,
on the cluster.
2. Run the reference validation perl script to produce a validated
reference.
3. Name the validated output and save it with the ".valid"
extension.
Example
/share/apps/corona/bin/reference_validation.pl -r
MY_REFERENCE.fasta -o MY_REFERENCE.fasta.valid
4. To ensure that the reference genome appears in the Reference
genome box of the Secondary Analysis Settings list, move the
reference genome file to the genomes folder, inside the
reference folder.
Example
mv MY_REFERENCE.fasta.valid
/share/reference/genomes/MY_REFERENCE.fasta
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