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Fix Sample Sheet

The Fix Sample Sheet page lets you correct errors in your sample sheet, or set up a new analysis to requeue.

You can resubmit the sample sheet and requeue the run with new analysis parameters up to five times.

1. From a Run summary page, select the Status drop-down list, point to Requeue, and then select Sample Sheet.

BaseSpace Sequence Hub validates the sample sheet and displays any errors above the sample sheet editor.

2. To make minor changes, edit the sample sheet in the sample sheet editor. BaseSpace Sequence Hub validates the sample sheet as you edit and displays any errors above the sample sheet editor.
3. To generate a new sample sheet or make complex changes, use the Illumina Experiment Manager.
  1. If you have not installed IEM yet, select the Illumina Experiment Manager (IEM) link, and install IEM.
  2. Open IEM.
  3. Import the original sample sheet from your system in IEM and edit it, or generate a new sample sheet. See the Illumina Experiment Manager User Guide for instructions.
  4. Copy and paste the sample sheet into the Sample Sheet Editor in BaseSpace Sequence Hub.
    BaseSpace Sequence Hub validates the sample sheet and displays any errors above the sample sheet editor.
4. When you have completed your changes and the sample sheet is valid, select Queue Analysis.

BaseSpace Sequence Hub analyzes the run using the new sample sheet.

NOTE

If your edits result in an invalid sample sheet, the Queue Analysis button is not available. You can return to the original using the Load Original button.

Genome Path Corrections

If a sample sheet is invalid, it could be because the genome path is not set up correctly. The paths of the standard BaseSpace Sequence Hub genomes must conform to the following relative paths:

Arabidopsis_thaliana\NCBI\build9.1\Sequence\WholeGenomeFASTA

Bos_taurus\Ensembl\UMD3.1\Sequence\WholeGenomeFASTA

Escherichia_coli_K_12_DH10B\NCBI\2008-03-17\Sequence\WholeGenomeFASTA

Homo_sapiens\UCSC\hg19\Sequence\WholeGenomeFASTA

Mus_musculus\UCSC\mm9\Sequence\WholeGenomeFASTA

PhiX\Illumina\RTA\Sequence\WholeGenomeFASTA

Rattus_norvegicus\UCSC\rn4\Sequence\WholeGenomeFASTA

Saccharomyces_cerevisiae\UCSC\sacCer2\Sequence\WholeGenomeFASTA

Staphylococcus_aureus_NCTC_8325\NCBI\2006-02-13\Sequence\WholeGenomeFASTA