1) To export constituent sequences in your project, first make the appropriate selection:
To export all of the constituent sequences for one or more contigs, either select the contig(s) in the Project Summary window or open the Alignment View for the contig of interest.
To export only some of the constituent sequences in a contig, select the sequence(s) you wish to export from the lower pane the Project Summary window|topic=The Project Summary Window.
To export the constituent sequences for part of a contig, go to the Alignment View and highlight a segment of the consensus sequence. The sequences that overlap that segment of the contig will be exported in their entirety.
2) Then, select Contig > Export Sequences. From the sub-menu, select either:
Single File - to export all of the sequences into one file.
Multiple Files - to export each sequence as an individual file.
Note: If you selected just one sequence, you may only choose Single File.
3) From the resulting Save dialog, choose the location, name (for a single file), and the desired file format from the list.
To save the sequence(s) with the gaps retained (not normally recommended) and/or features, check Include Gaps or Include Features. To save the sequence(s) with the gaps retained, check Include Gaps.
If you wish to export FASTA and Qual files for trace data files, select between FastA and Qual [Q] to export the Q scores and FastA and Qual [Q/N] to export the Q/n scores. Note that averaged quality scores (Q/n) are only applicable to trace data files.
Note: Selecting Include Gaps is not normally recommended, as a gap signifies no base in that location. If the box is not checked, SeqMan Pro will remove consensus gaps when the sequence(s) are saved.
4) Click Save to save the file(s).
When exporting constituent sequences, also note that:
•Exported sequences reflect any edits made to constituent sequences.
•If you choose to export FASTA and Qual files, the quality scores that are exported depend upon the type of files used for the assembly. For trace data, the qual file will contain either Q scores or Q/n scores for each base, depending on the format selected from the Format/Save as Type (Mac/Win) field. For flowgram data, the qual file will contain the imported quality scores.