User: jeremy.cox.2

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jeremy.cox.290
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Posts by jeremy.cox.2

<prev • 32 results • page 1 of 4 • next >
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Can I convert a species to otu?
... In one hand, I have OTU data from 16S, which can be graphed in a cladogram-like format. (My colleague generates this.) On the other hand, I have species counts, which can be graphed as a cladogram. I want to do a fair side-by-side comparison. I am pretty sure we can't convert OTU to species or g ...
otu 16s taxonomy written 19 months ago by jeremy.cox.290 • updated 10 months ago by lakhujanivijay4.3k
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Comment: C: Suggestions on Sharing VERY LARGE files?
... Good question. I could offer smaller versions of the database, but I fear some people will want "the whole enchillada" as it were. Previewing the database through the web is also an excellent suggestion. But for high volume computations, they'll want to download database and use their own machines ...
written 2.8 years ago by jeremy.cox.290
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Comment: C: Accession number to taxonomy id after blasting
... It worked like magic. Thanks ...
written 2.8 years ago by jeremy.cox.290
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Comment: C: Find highly similar regions of specific lengths to a query in a genome
... I suppose I should go one step further. If that is the case, would querying against all possible subsequences solve the problem? Two short PERL or Python scripts would do the trick. One to make the new queries with informative query names, and then one to summarize all the results to find matches ...
written 2.8 years ago by jeremy.cox.290
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Answer: A: Accession number to taxonomy id after blasting
... It is hard to understand your exact problem without an example BLAST outformat 6 line. However, I routinely do this sort of conversion, and with some minimal programming you can convert this. If your database is built from NCBI database, then the Accession number should be in the reference seque ...
written 2.8 years ago by jeremy.cox.290
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Comment: C: Find highly similar regions of specific lengths to a query in a genome
... I want to make sure I understand the question: So you would like to take a query sequence longer than 150bp, and then try to find high percent identity matches to any subsequence 150bp long? So, then, there would be 51 possible subsequences of length 150 in a query that is 200 bp long. ...
written 2.8 years ago by jeremy.cox.290
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Suggestions on Sharing VERY LARGE files?
... I am building a large database for my analysis tool ~3 Terabytes. The issue is distributing this database for people to use it. A solution we have learned from working with sequencing cores is to ship a hard drive by FedEx. A possibly expensive and annoying proposition. Another solution is to ...
hosting files written 2.8 years ago by jeremy.cox.290 • updated 2.8 years ago by dyollluap300
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Comment: C: How to create a GO Network in Cytoscape?
... Your answer was helpful, thank you. I ultimately made a script to generate the network! The key problem was I didn't have ANY genes identified, not that I don't have network information for them. The organisms I am studying don't have annotated genes. So I literally only have GO terms to build a ...
written 3.2 years ago by jeremy.cox.290
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Answer: A: How to create a GO Network in Cytoscape?
... This is how I accomplished the task of making the GO network in Cytoscape. 1) Download go.obo from http://geneontology.org/page/download-ontology 2) Run my python script to convert go.obo to GO.cytoscape.sif file 3) Cytoscape -> Import -> Network -> File, select the GO.cytoscape.sif file ...
written 3.2 years ago by jeremy.cox.290
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Comment: C: How to create a GO Network in Cytoscape?
... [Gene ontology tool list][1] has helped. I found GOBU there... which allows me to import GO terms. Problem is, the manual doesn't specify their custom file format. I think I could simply create my own tree using the go.obo data file. Then I just need to put into a format Cytoscape understands. ...
written 3.2 years ago by jeremy.cox.290

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