Hello Thomas,

Using Tophat would be fine. To understand the parameters used, click on the "i" icon in the job run's dataset box in the history. For certain tools, this is also captured (line command) in the "Info:" field after the job completes.


Take care,

Jen
Galaxy team

On 8/9/11 1:28 AM, Thomas Jenner Pulikotial Augustine wrote:
Hi,

I would like to know whether i should use Tophat or LASTZ for
transcriptome analysis, the reads(transcriptome) were obtain from 454 GS
flx sequencer. Kindly reply, in the FAQ section we're suggested to use
Tophat but this was designed for Illumina genome analyzer. Thanks in
advance.

Br,
Thomas

On Mon, Aug 8, 2011 at 1:40 PM, Thomas Jenner Pulikotial Augustine
<pulikot...@gmail.com <mailto:pulikot...@gmail.com>> wrote:

    Hi,

    I would like to know the default options used by Galaxy to align 454
    reads to reference genome using LASTZ alignment software. I'm trying
    to align the query to a reference genome, kindly tell the me list of
    options used for aligning the reads to reference genome. An
    additional question, does Galaxy share scripts? i can across a link
    that seems to be sharing scripts.

    Br,
    Thomas


    On Sat, Jul 30, 2011 at 1:44 AM, Jennifer Jackson <j...@bx.psu.edu
    <mailto:j...@bx.psu.edu>> wrote:

        Hello Thomas,

        For 454 data, there is a specific screencast that may be of
        interest. Go to http://usegalaxy.org and scroll in the middle
        pane to find quickie #15.

        We have had very high usage over the last few days, but have
        since been able to clear out more resource. Your job will likely
        start within the next 24 hrs.

        Hopefully this helps,

        Thank you!

        Jen
        Galaxy team


        On 7/29/11 4:18 AM, Thomas Jenner Pulikotial Augustine wrote:

            Hi,

            I'm trying to map a data set containing 454 reads to a
            reference genome
            using LASTZ alignment package in Galaxy. I'm following a
            workflow used
            for Illumina reads with the only change in the alignment
            package, i'm
            using LASTZ instead of bowtie/bwa. The following is the
            procedure please
            correct me if it's wrong and do suggest any additional
            procedure to make
            the workflow better.

            In addition to this i'm, trying to do metagenomics analysis
            as well
            by following the procedure given in one of the video
            tutorials. I've
            submitted the files for alignment and its been a day since the
            submission and the process has not yet started, could you
            tell me what
            could be the reason. The file size is 110Mb, under history
            the package
            indicate "Job is waiting run"  how long does it usually take
            to initiate
            the process in the queue. Your suggestion's are valuable,
            thanks for
            developing Galaxy.

            Kindly help, thank you.

            1.Uploaded a FASTA file as input
            2.Align using LASTZ
            3.Filtering SAM files on bit-wise flag values
            4.Finding how many reads are mapped to each chromosome
            5.Sort the read counts
            6.convert sam to bam
            7.perform flagstat operation

            Br,
            Thomas


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        --
        Jennifer Jackson
        http://usegalaxy.org
        http://galaxyproject.org/__Support
        <http://galaxyproject.org/Support>




--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
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