User: Fiamh

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Fiamh220
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Posts by Fiamh

<prev • 7 results • page 1 of 1 • next >
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Comment: C: What Assembler To Use For Eukaryotes?
... Ketil, realize that -- but from what I can tell you are in mostly uncharted territory, something reflected by Ewan's comments. Short of hunting down people struggling with the same problem you'll probably have a hard time finding success stories. The SeqAnswers forum might be a better place of resea ...
written 9.1 years ago by Fiamh220
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Answer: A: What Assembler To Use For Eukaryotes?
... Did you see Ewan's summary? Along with comments at Gattaca: Velvet's algorithms in theory work for any size. However, the engineering aspects of Velvet, in particular memory consumption, means it's unable to handle read sets of a particular size. This of course depends on how big a real memory mach ...
written 9.1 years ago by Fiamh220
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Comment: C: Transcription Factor Enrichment
... In that case a number of systems such as CisRed won't make sense to use as they have their own, fixed definition of start sites and promoters. The second question would be just how many promoters do you have. If it's just a few you probably have to revert to systems that use phylogenetic footprintin ...
written 9.1 years ago by Fiamh220
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Answer: A: 454 Coverage Quality
... As Istvan pointed out it depends heavily on the extraction approach. The figure I've seen mentioned most consistently is even lower at 80-90% (for example see [Dan's recent report from the CSHL meeting][1]). [1]: http://www.massgenomics.org/2010/09/cshl-2010-genomes-get-personal.html) ...
written 9.1 years ago by Fiamh220 • updated 11 weeks ago by RamRS24k
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Answer: A: Transcription Factor Enrichment
... That's actually one major difference between the various tools -- Dave, do you have a list of genes or promoter sequences? Many tools expect a list of genes because they have their own concept of what a promoter is. If you have CAGE or RNA-Seq data and would like to define which promoter you are int ...
written 9.1 years ago by Fiamh220
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Answer: A: Transcription Factor Enrichment
... I'd second MEME as a conservative approach. Try to see which patterns are stable over a range of promoter sizes, promoter subsets and cutoffs. Once you have those switch to TOMTOM (part of the MEME suite) to map it to JASPER or TRANSFAC matrices. ...
written 9.1 years ago by Fiamh220
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Answer: A: C/C++ Libraries For Bioinformatics?
... Can I pitch Curtis Huttenhower's [Sleipnir library][1]? (Tutorial [here][2]) -- Oliver [1]: http://huttenhower.sph.harvard.edu/sleipnir/ [2]: http://www.huttenhower.org/content/getting-started-sleipnir ...
written 9.4 years ago by Fiamh220 • updated 14 months ago by RamRS24k

Latest awards to Fiamh

Appreciated 9.1 years ago, created a post with more than 5 votes. For A: What Assembler To Use For Eukaryotes?
Good Answer 9.1 years ago, created an answer that was upvoted at least 5 times. For A: What Assembler To Use For Eukaryotes?
Teacher 9.1 years ago, created an answer with at least 3 up-votes. For A: What Assembler To Use For Eukaryotes?
Teacher 9.4 years ago, created an answer with at least 3 up-votes. For A: C/C++ Libraries For Bioinformatics?

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