Hello,
I will be analyzing a relatively large targeted resequencing data set (paired variant calling) and I wondered how would be the best way for the "wet lab" people to display and understand the results. After all, I can't quite give them VCF files and hope they can understand them...
So I'm interested in suggestions for software for visualization and perhaps something that could help interpretation, too. IGV comes to mind, but web based tools (especially if they can be self hosted) would be good as well.
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Luca Beltrame
If you are willing to try commercial software - our Enlis Genome Research package was designed with "wet lab" people in mind. ( http://www.enlis.com/research_edition.html )
Devonj,
I have not used your software before but it seems to be a powerful "easy handle" tools from what I browsed on your website. I could not find information like how much it costs, but I will try to use the trial version whenever my data are ready.
IGV. And it's free. And there are lots of tutorials/walkthroughs; Broad has some nice ones derived from their workshops.
EDIT: Should also mention GenomeView as well.
we have found IGV very useful for visualizing all NGS data that is provided to users. loading BAM alignment, BIGWIG coverages, VCF and GFF variants, BED regions,... all in 1 place is definitely convenient.
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I dont know what exactly you are looking for but you can try UCSC genome browser or lookseq.
The visualizations that will be most useful depend to a huge extent upon the design of the study. There are many, many things you might want to explore in this data, so you're going to have to narrow it down to get reasonable recommendations.