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  • edge
    Senior Member
    • Sep 2009
    • 199
    #1

    MIRA3: Create Scaffold Fasta files problem

    Hi,

    Regarding the paper "Instructions for scaffolding MIRA 454 contigs & 25 KB paired-end data with BAMBUS", I would like to ask some comments about the section "Create Scaffold Fasta File".
    Based on the command below:
    printScaff -e non_O157_bambus.evidence.xml -s non_O157_bambus.out.xml -l
    non_O157_bambus.lib -f non_0157_out.unpadded.fasta -merge -o
    non_O157_bambus_scaffold -page -dot

    Can I know how to create the non_0157_out.unpadded.fasta? Or this file refer what?
    I got read the this website
    AMOS
    http://sourceforge.net/apps/mediawiki/amos/index.php?title=Bambus_Manual#Getting_more_.28or_less.29_information_from_the_output
    Download AMOS for free. AMOS is a collection of tools for genome assembly. AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.

    But still quite confusing about the way to create the non_0157_out.unpadded.fasta -merge.
    Actually based on the command above, non_0157_out.unpadded.fasta is the input or output file?
    How to obtain the non_0157_out.unpadded.fasta file below I running the printScaff command.
    Thanks a lot for all of your advice.
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