Miseq illumina software or Galaxy platform
I want to know if I could uses the built in software in Miseq illumina for detecting variation like indels or snps and allignment and other issues (next generation sequencing) I want to know advantages and disadvantages or it is better to use third party software like Galaxy Platform for Genomics?
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Abdelazeem_abdelhameed2015505 •
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Do you have any experience with this kind of work or someone else in your institution who can guide you? What type of analysis do you aim to achieve? How much data do you have to process?
No experience , the research would aim to recalling variants and detecting mutations in specific genes
See the answer of genomax2 then ;-) Galaxy has many options, so when you have a research question you cannot answer using Miseq software, galaxy would be worth trying.
If you do not have access to other IT infrastructure (and/or your have no experience working with unix/command line) then you could definitely use MiSeq reporter for this analysis.
Specific advantages or disadvantages of one method over something else are hard to recap without additional information about what you are trying to do. If you are looking to do simple analysis then the canned workflow in MiSeq reporter may be adequate for your needs.