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Question: Workflow Assistance
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gravatar for Kevin Pawlik PhD
7.4 years ago by
Kevin Pawlik PhD • 10
Kevin Pawlik PhD • 10 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
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modified 7.4 years ago by Anton Nekrutenko ♦ 1.7k • written 7.4 years ago by Kevin Pawlik PhD • 10
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gravatar for Anton Nekrutenko
7.4 years ago by
Anton Nekrutenko ♦ 1.7k
Penn State
Anton Nekrutenko ♦ 1.7k wrote:
Kevin: Is this a diploid or haploid organism? anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
ADD COMMENT • link written 7.4 years ago by Anton Nekrutenko ♦ 1.7k
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gravatar for Anton Nekrutenko
7.4 years ago by
Anton Nekrutenko ♦ 1.7k
Penn State
Anton Nekrutenko ♦ 1.7k 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 COMMENT • link written 7.4 years ago by Anton Nekrutenko ♦ 1.7k
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