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  • kmcarr
    replied
    gaster,

    Are you using the Roche GUI (gsAssembler) to view the 454AlignmentInfo.tsv? If so this viewer truncates the display at 50,000 lines. The file is located in the assembly subdirectory of your main project directory. You can view the entire file with a standard text editor. (Careful, if your assembly is large this file will get huge.) You will need to process the file using some sort of script to extract and calculate the coverage information you asked about (ave, min, max, etc.).

    Leave a comment:


  • sklages
    replied
    The 454NewblerMetrics.txt reports only common stats about the assembly.

    Well, and the tsv file covers all contigs:

    Code:
    $ fgrep -c \>contig 454AlignmentInfo.tsv
    430
    $ fgrep -c \> 454AllContigs.fna
    430
    cheers,
    Sven

    Leave a comment:


  • gaster
    replied
    Thanks, Sklages. The metrics files don't seem to have info about coverage, right?

    The 454AlignmentInfo.tsz files only gives me partial info on one contig. Is that right? It can't be. Any ideas?

    Thanks so much.

    Leave a comment:


  • gaster
    replied
    Thanks for your reply, Flxlex. Couple questions: How do you set the g-flag? Is there no way to get min/max coverage?

    Thanks.

    Leave a comment:


  • flxlex
    replied
    And/or have newbler produce the 454ContigGraph.txt file which gives you average coverage per contig (not min/max). This can be done by setting the -g flag (note: this sets the minimum contig length to report from 100 bp to 1 bp...).

    Leave a comment:


  • sklages
    replied
    Hi,

    you might want to have a look at 454NewblerMetrics.txt (or csv) for assembly statistics and 454ReadStatus.txt to see what happened to your reads ...

    A detailed contig description (for parsing) gives you 454AlignmentInfo.tsv .

    hth,
    Sven

    Leave a comment:


  • gaster
    started a topic Summary Statistics in Newbler?

    Summary Statistics in Newbler?

    The Mapper output comes with handy xls file with a lot of great statistics in it. The Newbler output doesn't seem to have anything like this? I am particularly looking for statistics about the coverage in the contigs (avg, min, max, etc.)

    Anyone know where this info is or a good program to use to find it?

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