Use File->Export in the Contig Editor to save selected reads

Last week we covered the fact that you can use File->Export to save sequences or alignments in different formats. Delving down deeper into this, some of the views will save different types of data based on what you select in the format menu. The best example of this is the Contig Editor. If you choose File->Export… in this window you get the following File Format options;


  • MacVector Reference Assembly – this saves a copy of the alignment in MacVector format. It is the same as choosing File->Save As….
  • MacVector NA Sequence – this saves the Reference sequence only as a MacVector formatted .nucl file. If you have edited the Reference, this is the easy way to save a copy of it under a new filename.
  • FASTA Multiple Sequence – this saves any selected reads into a single fasta-formatted multiple sequence file. Use this if you have aligned a large number of sequences and want to save a subset of them into a single file for additional analysis (e.g. assembly).
  • FASTQ Multiple Sequence – similar to the fasta option, but saves in fastq format. This format includes quality information.
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