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  • Gff, moving assemblies and other things

    Hello everyone,

    This being my first post please excuse any newbie mistake I might make on format or such.
    Currently I'm working with a cDNA run from the 454 GSFLX Titanium and have already done an assembly with GS De Novo and an assembly with GS reference mapper. First order of business is:

    1) I need to move the file from one computer with the programs installed to another, problem is copy/paste doesn't seem to be the best option considering file are not in the same directories in one pc to another. Is there any way to edit the orginal location once I moved them and opened them in the new PC? Has any of you encountered this and done it differently? Any help will be welcomed.

    Second order of business has to do with a .gff annotation file. It's the file that came with the reference .fna file used with the reference mapper and I'm pretty sure it has the correct format inside since I opened it and saw it but sill every time I add it to the GUI and try to run it says:

    Warning: Could not open /directory/of/annotation/file.gff
    Warning: Unknown format in gene annotation file: /directory/of/annotation/file.gff, line#1, Skipping...
    (it does this for the next 10 lines until it says that:
    Warning: Gene annotation file contains many lines with unknown formatting.
    Error: Unable to parse Known Genes file: /directory/of/annotation/file.gff

    So far I opened the file and it seems to be alright, if needed I could post the first few lines. Any further details needed just ask and thanks in anticipation.

    Confused, :S
    BXLion

  • #2
    Hi,

    I have the same problem that BXLion mentioned above (2nd question). Which is the correct file format input for annotation information in the gsmapper (454)? I have a .gff file with gene features from genbank (I did the convertion .gb to .gff using this tool: http://www-bimas.cit.nih.gov/molbio/readseq/), but I'm not sure if this is the correct format. I read about the GenePred (.gp) format in some foruns, and I hope that this is the best format, but I can convert .gff to GenePred format. Does anyone has some tip to solve this issue?

    Best

    Comment

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