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 <pulikotial@gmail.com <mailto:pulikotial@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 <jen@bx.psu.edu <mailto:jen@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

_____________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org <http://usegalaxy.org>. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/__listinfo/galaxy-dev <http://lists.bx.psu.edu/listinfo/galaxy-dev>

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

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

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