To load the sample data files
You can load a data file as-is only if the data file is in BAM format or in .fasta format, which includes Roche .fna files and SOLiD System .csfasta files. With the exception of the BAM format, if the data file is not in .fasta format, you must convert the file to the .fasta format before loading it. (See The NextGENe Format Conversion Tool.)
 | Preprocessing of files must also be necessary before you can load the files. For example, if you used barcoding or multiplexing, then you must sort the data before you can load it. Be aware of any preprocessing that you must carry out before you can covert and/or load sample and/or reference files. |
1. Click Next or Load Data.
The Load Data page opens.
2. In the Sample Files pane, click Load.
| | By default, .fasta is the selected file type. To process BAM files, you must select BAM files as the file type. |
3. In the Open dialog box, browse to and select the data file that you analyzing, and then click Open to load the selected file in to the Project Wizard.
| | A data file in the .fasta format has a file extension of “.fasta,” “.fna,” or “.csfasta.” The name of a data file that has been converted to the .fasta format by NextGENe’s Format Conversion tool is appended with the phrase “_converted.” |
| | You can load multiple data files for the same single sequence read project. If you are using the Somatic Mutation Comparison tool to analyze your data, then SoftGenetics recommends a minimum of four normal samples to create a single pooled project. See The Somatic Mutation Comparison tool. |
4. Do one of the following:
• If you loaded an aligned BAM file, and you want to realign the data, then leave Realignment (below the Output field) selected, and then go to Step 5.
• If you loaded an aligned BAM file, but you do not want to realign the data in the file, then clear the Realignment option, and then go to Step 5..
5. Do one of the following:
• If you selected the de novo Assembly application type, then continue to To specify the output file name and location.
• If you selected any other application type other than cde novo Assembly, then continue to To load the reference files.