Question: Re: Ngs Mapping Using Lastz
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gravatar for Thomas Jenner Pulikotial Augustine
7.3 years ago by
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
bwa alignment bowtie • 1.2k views
ADD COMMENTlink modified 7.3 years ago by Jennifer Hillman Jackson25k • written 7.3 years ago by Thomas Jenner Pulikotial Augustine10
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gravatar for Jennifer Hillman Jackson
7.3 years ago by
United States
Jennifer Hillman Jackson25k 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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENTlink written 7.3 years ago by Jennifer Hillman Jackson25k
0
gravatar for Jennifer Hillman Jackson
7.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:
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 -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENTlink written 7.3 years ago by Jennifer Hillman Jackson25k
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