For read simulation, you may also want to give Grinder a try. I made a Galaxy wrapper for it (see in the toolshed: http://toolshed.g2.bx.psu.edu/)
Florent

On 20/09/11 18:46, Kevin Lam wrote:
Hi Daniel,
You would have multiple names for each sequence and that would be quite hard to display. I am sure someone thought through this. Since the sequence is the same, you can use the sequence to look back in the fastq file for read name. Although I am not sure how that would help you?


Cheers
Kevin


On 20 September 2011 13:43, Daniel Sher <ds...@sci.haifa.ac.il <mailto:ds...@sci.haifa.ac.il>> wrote:

    Thanks Kevin.  However, the collapse sequences replaces the
    original name of the sequences with a numerical code, and I need
    to keep the original names.  Any other suggestions?

    Thanks

    Daniel

    On 20/09/2011 05:32, Kevin Lam wrote:
    Hi Daniel
    for 2) you may use the tools under NGS QC and manipulation
    FASTQ to FASTA
    <http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastq_to_fasta>
    converter

    followed by

    Collapse
    <http://main.g2.bx.psu.edu/tool_runner?tool_id=cshl_fastx_collapser>
    sequences


    On 19 September 2011 09:54, Kevin Lam <ke...@aitbiotech.com
    <mailto:ke...@aitbiotech.com>> wrote:

        For 1) you may refer to


              Simulated Dataset of Solexa - SEQanswers
              <http://seqanswers.com/forums/showthread.php?t=806>



        Has anyone replied you for 2) ?



        On 18 September 2011 21:12, Daniel Sher
        <ds...@sci.haifa.ac.il <mailto:ds...@sci.haifa.ac.il>> wrote:

            Hello,

            I have two questions - I apologize if they are trivial..

            1) I want to simulate the amount of Illumina sequencing
            needed to sequence  and assemble a known genome.  Is
            there a way to randomly pick sequences of a specific
            length from a genome (either one available online or one
            I upload)?  Something like "pick 100bp randomly (either
            strand), move 400-500bp forward and pick another 100bp?"

            2) Is there a way to remove redundant sequences from a
            FASTA file without losing the original sequence names (as
            happens with "collapse")?

            Thanks

            Daniel


-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
            Daniel Sher, PhD
            Department of Marine Biology
            Leon H. Charney School of Marine Sciences
            University of Haifa, Mt. Carmel 31905, Haifa, Israel

            Office+972-4-8240731  <tel:%2B972-4-8240731>
            Lab+972-4-8288961  <tel:%2B972-4-8288961>
            email:ds...@sci.haifa.ac.il  <mailto:ds...@sci.haifa.ac.il>


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-- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Daniel Sher, PhD
    Department of Marine Biology
    Leon H. Charney School of Marine Sciences
    University of Haifa, Mt. Carmel 31905, Haifa, Israel

    Office+972-4-8240731  <tel:%2B972-4-8240731>
    Lab+972-4-8288961  <tel:%2B972-4-8288961>
    email:ds...@sci.haifa.ac.il  <mailto:ds...@sci.haifa.ac.il>



___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
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please use the interface at:

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