Editing the content of an ab1 file

thedamian · 03-20-2012, 01:04 AM

Hi,
Is there any command-line application (a script) that allows editing/changing metadata inside an .ab1 file?

I'm using DNA Analyzer 3730 Data Collection Software v3.0 and Applied Biosystems DNA Sequencing Analysis Software 5.1 but these software don't allow to load any list of sample names for sample editing. Every time I need to change names manually (for 96 well plate it is a nightmare).

Vinz · 04-12-2012, 06:00 AM

You should not need to change the ab1 file.
Go to the plate manager. There you import the plate information. The file for import is a simple tab separated text file. Just export one of your plates for a start. Now you may open it with excel and change sample names or whatever you need to change. Obviously you may also create those files by scripts...
I hope this helps...

thedamian · 04-12-2012, 06:42 AM

Yes, that's the regular way to do it. But I am wondering what to do when the sample list that I have imported from tab delimited file to plate manager is mistaken and my run is already done and I have abi files with wrong names inside meta data.
Every time it is the case I have to manually change the sample names in "run history/ reextraction" section.
I would be easier to upload the csv or other file with new proper name.
Or maybe there is another software to do it in bulk?

Vinz · 04-12-2012, 07:14 AM

If you know perl you may use the write_tag() method of the Bio::Trace::ABIF module.
Are you using the barcode option to make sure not to mix up the plates? I would highly recommend that.

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03-20-2012, 01:04 AM	#1
thedamian Member Location: Warsaw Join Date: Feb 2012 Posts: 34	Editing the content of an ab1 file Hi, Is there any command-line application (a script) that allows editing/changing metadata inside an .ab1 file? I'm using DNA Analyzer 3730 Data Collection Software v3.0 and Applied Biosystems DNA Sequencing Analysis Software 5.1 but these software don't allow to load any list of sample names for sample editing. Every time I need to change names manually (for 96 well plate it is a nightmare).

04-12-2012, 06:00 AM	#2
Vinz Member Location: Germany Join Date: Dec 2010 Posts: 53	You should not need to change the ab1 file. Go to the plate manager. There you import the plate information. The file for import is a simple tab separated text file. Just export one of your plates for a start. Now you may open it with excel and change sample names or whatever you need to change. Obviously you may also create those files by scripts... I hope this helps...

04-12-2012, 06:42 AM	#3
thedamian Member Location: Warsaw Join Date: Feb 2012 Posts: 34	Yes, that's the regular way to do it. But I am wondering what to do when the sample list that I have imported from tab delimited file to plate manager is mistaken and my run is already done and I have abi files with wrong names inside meta data. Every time it is the case I have to manually change the sample names in "run history/ reextraction" section. I would be easier to upload the csv or other file with new proper name. Or maybe there is another software to do it in bulk?

04-12-2012, 07:14 AM	#4
Vinz Member Location: Germany Join Date: Dec 2010 Posts: 53	If you know perl you may use the write_tag() method of the Bio::Trace::ABIF module. Are you using the barcode option to make sure not to mix up the plates? I would highly recommend that.