User: Ricardo A.
Ricardo A. • 90
- Reputation:
- 90
- Status:
- Trusted
- Location:
- University of Michigan Ann Arbor, MI - USA
- Twitter:
- rdalbanus
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 month, 3 weeks ago
- Joined:
- 7 months, 2 weeks ago
- Email:
- r********@gmail.com
PhD Candidate - Dept. of Computational Medicine & Bioinformatics. University of Michigan
Posts by Ricardo A.
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... #### Question
Does anyone here has had any experience using GC content isochores in GAT? It would be great to hear your experiences with this feature.
#### Issues with isochores
Using isochores is not very well documented in the manual and I'm having trouble determining how to build and use the inp ...
written 12 weeks ago by
Ricardo A. • 90
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... A while back I found this list of free open access journals: http://www.conem.org/links/resources-authors/oaj-selected/
Depending on the topic of your dataset, you can find a potential good fit in one of those. ...
written 7 months ago by
Ricardo A. • 90
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... I think it makes sense to use smaller shift and extension in this case. Why are you only looking at small fragments? There is a lot of information on larger mono and dinucleosome-sized fragments. ...
written 7 months ago by
Ricardo A. • 90
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... Hi, josruirod,
The `--nomodel` flag will tell MACS2 to bypass the model building, which would calculate the `shift`/`extsize` parameters. Since you are asking it to use the fragment information from the paired reads, then it doesn't need to figure out a model as it already have the information from ...
written 7 months ago by
Ricardo A. • 90
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... Hi, Ishack,
I believe you should be able to get some good amount of experience during your Masters. Do you have something like required research credits? I'd imagine that you could fulfill those by doing an internship (that's what a significant part of our masters students do here in Michigan). Int ...
written 7 months ago by
Ricardo A. • 90
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Answer:
A: BagFoot TF foot printing
... **EDIT**: I called victory too soon... It took me two full days to figure out why this package would not run on our data. It was the first time I've ever had to really use the debugging functions in RStudio (thanks, Hadley!). After extensive tinkering and innumerous tracebacks, I found that the prob ...
written 7 months ago by
Ricardo A. • 90
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