Question: Workflow Assistance
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gravatar for Kevin Pawlik PhD
7.4 years ago by
Kevin Pawlik PhD10 wrote:
After viewing tutorials and reading the information associated with various tools, I ask that you point me toward an appropriate workflow for the following: I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed Bowtie alignments. I want to find the allelic positions where the (+) genomes differ from the (-) genome. Many thanks, Kevin
alignment bowtie • 882 views
ADD COMMENTlink modified 7.4 years ago by Anton Nekrutenko1.7k • written 7.4 years ago by Kevin Pawlik PhD10
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gravatar for Anton Nekrutenko
7.4 years ago by
Penn State
Anton Nekrutenko1.7k wrote:
Kevin: Is this a diploid or haploid organism? anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
ADD COMMENTlink written 7.4 years ago by Anton Nekrutenko1.7k
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gravatar for Anton Nekrutenko
7.4 years ago by
Penn State
Anton Nekrutenko1.7k wrote:
Kevin: Yes, for Illumina data BWA would be the best option from what is currently available at the main site. You can then identify variants with pileup and compare across the samples much as it is shown at http://usegalaxy.org/heteroplasmy. This should give you a rough idea on what to expect. However, piplines for proper (1000genomes-like) varinat calling that include realignment and recalibration steps are coming by the end of the Summer. Thanks! anton Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
ADD COMMENTlink written 7.4 years ago by Anton Nekrutenko1.7k
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