454 gsAmplicon Editing Reads

[styagi]

Does anyone know how to edit reads after alignment has been done using gsAmplicon software? I want to go back and edit any variants that I know are sequencing errors.

[styagi]

I just found that there is no function to edit reads on the 454 software. Does anyone know a program that would allow me to edit reads post alignment. I dont want filter out the reads completely, I want to be able to edit the errors and use them for alignment and analysis.

[Zaag]

Well if that really is what you want you could go from sff to fasta, alter the fasta and go back to sff. You can use the sfftools/sffinfo provided by Roche.

[styagi]

I thought sfftools was only provided with the 454 machine which I dont have. I had my samples sequenced at a core bioinformatics lab.

[Zaag]

From what I understand they'll give you the programs you need if you ask nicely:

http://seqanswers.com/forums/showpost.php?p=8278&postcount=13

I think there also are some open source variants of the tools but I never used them.

[styagi]

I will look into that.
thank you for your help!

[martin2]

Well if that really is what you want you could go from sff to fasta, alter the fasta and go back to sff. You can use the sfftools/sffinfo provided by Roche.

You can't go back from FASTA/Q and re-create SFF. In theory you could but nobody wrote such code yet. As far as I am aware of the status in biopython, Roche sfftools, flower.