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Recent Activity
All posts created by DanRussell
Link to this post | posted 17 Jan, 2017 20:59 | |
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Hi Greg, You actually want Hyper-V turned OFF, not on, so I don't think it is an issue that some hardware setups don't allow it. The second step in the instructions above is usually the one that needs to be rectified, and Windows 10 Home users should still be able to do that. –Dan |
Link to this post | posted 01 Dec, 2016 16:25 | |
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Hi all, We switched the SEA Virtual Machine to be 64-bit this year instead of 32-bit, and one unintended side-effect is that on some Windows computers, you'll have to make one or two changes to be able to install the VM. If you'd like this in document version it's at the link below. Instructions to enable 64-bit Ubuntu in Virtual Box Now here's the fix itself… PROBLEM: After installing Virtual Box on Windows, there is no “Ubuntu (64-bit)” option in the dropdown menu, only “Ubuntu (32-bit)”. There are two steps below that should fix this and allow you to select a 64-bit option for your VM installation. The first step can be done from within Windows fairly quickly. If that doesn’t work, the second step required entering your system’s BIOS, so we recommend trying the first one, then moving on to the second only if necessary. Step 1: Change Hyper-V settings (easier fix)
Step 2: Enable Intel virtualization (more complicated fix)
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Link to this post | posted 17 Nov, 2016 17:00 | |
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Nicholas Edgington Hey Nick, We haven't tried that in any real experimental way. We do sometimes get samples with host DNA contamination, and in most cases it's relatively low coverage compared to the phage and thus isn't a problem. On the other hand, we have seen a few samples where the host coverage was high enough to drop the phage coverage to an unusable/undetectable level. So I guess: who knows? Also, has anyone tried side-by-side old protocol versus new protocol to check for yields from each? That would perhaps shed some light. Having a high titer is certainly the most important thing to getting good yield, so bumping up the titer wherever possible is probably the best way to help. –Dan |
Link to this post | posted 16 Nov, 2016 15:12 | |
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Hi all, Since we at Pitt are receiving DNA samples for sequencing (and thus gel pictures as well) I can say that we're seeing more smeary degraded stuff this year than in the past. Not sure what's going on, but I don't think it's limited to 1-2 schools. –Dan |
Link to this post | posted 16 Nov, 2016 15:08 | |
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Hi all, If you're experiencing recent problems with DNA Master, it's probably because of the update of NCBI to use secure connections. See the blog post and forum below, but the gist of it is that DNA Master was updated on Nov 15, 2016 to be able to handle this, so if you haven't updated your DNA Master since then, please do so! http://seaphages.org/blog/2016/11/16/dna-master-updated-use-secure-ncbi-connections/ http://seaphages.org/forums/topic/214/ –Dan |
Posted in: DNA Master → Glimmer Failure on Auto Annotation
Link to this post | posted 16 Nov, 2016 15:06 | |
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New as of November 15, 2016 Some very important changes have been made to DNA Master to accommodate NCBI's new secure https protocols. Versions of DNA Master from before this date will not be able to connect to NCBI and thus will not be able to auto-annotate genomes or run BLAST. Updating your DNA Master will allow you to be able to use NCBI's new protocols. See this blog post for more information. http://seaphages.org/blog/2016/11/16/dna-master-updated-use-secure-ncbi-connections/ –Dan |
Posted in: DNA Master → Important DNA Master Update
Link to this post | posted 15 Sep, 2016 20:41 | |
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Shallee Page Hey Shallee, Don't know if you're heading for DNA Master in general, but there's a forum topic here for that. There's also a new document about DNA Master on Mac. (The XQuartz part will probably be relevant to any WINE program, but the other stuff is DNA Master-specific.) –Dan |
Posted in: SEA-PHAGES Virtual Machine → WINE
Link to this post | posted 13 Sep, 2016 19:18 | |
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Hi all, Attached to this message (and linked here) is a document describing the project. –Dan |
Posted in: Xeno Project → Basic Xeno Project Information
Link to this post | posted 13 Sep, 2016 19:14 | |
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Hi all, Attached to this message (and linked here) is a document describing the project. –Dan |
Posted in: Host-Range Project → Basic Host Range Project Information
Link to this post | posted 13 Sep, 2016 18:41 | |
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This forum is primarily meant to be a container for all the different sub-forums that will contain information about annotating specific clusters and subclusters of phages. While everyone was trained in general to do phage annotations, there are certain things that might be of particular interest given the particular cluster you end up annotating. Cluster M? It'd be good to know about tRNAs! Cluster G? Look out for mobile elements! If you have questions about a particular phage/group, please ask them in the appropriate sub-forum. Good luck! –Dan |
Posted in: Cluster-Specific Annotation Tips → Using This Forum