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  • martin2
    replied
    Originally posted by Zaag View Post
    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.

    Leave a comment:


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

    Leave a comment:


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

    Pyrosequencing in picotiter plates, custom arrays for enrichment/decomplexing. (Roche)


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

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

    Leave a comment:


  • Zaag
    replied
    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.

    Leave a comment:


  • styagi
    replied
    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.

    Leave a comment:


  • styagi
    started a topic 454 gsAmplicon Editing Reads

    454 gsAmplicon Editing Reads

    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.

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