converting Beckman CEQ 8000 Sequencer files to ABI/SCF

[raymnl96]

Hello...my sequence files are saved as .cqx files. Does anyone know how I can convert them to fasta files so I am able to use DNA Baser. I am currently using a Beckman CEQ 8000 Sequencer and I can only save files as .cqx or .txt. Thanks for any help!

[admin]

When data is collected on the CEQ8000 it will always be in format .cqs.
However you can export your data files in other formats for viewing in 3rd party softwares. The easiest way to do this is from the datamanager as follows:

1) Open up the datamanager


Double click on your active database to view the 'Default' project


Double click on the Default project to view a series of folders.


Click on 'Sequence Results' folder to display all sequence result files in your database.


Highlight all sequence files that you want to export then right mouse click and select 'Export'


Choose a location to save your files to e.g. Desktop and then click Save as Type dropdown. As format, select SCF and then click 'Export'


This will export a copy of your data files in the desired format.

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Also, have you looked into those TXT files? Maybe they are just FASTA file but with wrong extension. It happens often. Try to assemble those TXT files with DNA Baser. In the worst case, DNA Baser will crash (there is nothing dangerous in this, just restart the program). In the best case, you will get a contig

IMPORTANT: please note that the recommended format for DNA Baser is SCF or ABI (with quality values included). If you use one of these formats, DNA Baser Assembler will be able to automate the contig assembly process. As a result, your contigs will be ready faster, they will be more accurate and you will not have to correct manually the ambiguities (mismatches).