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JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by edgingtonn1
Link to this post | posted 10 Apr, 2017 14:32 | |
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Hi, It seems that the Z-scores from PECAAN differ from the Z-scores from DNAMaster for a given gene, and for the same start sites. Any idea why? Both scores for the same gene start always seem to show the same trend, so it doesn't seem like a big issue– just a curiosity for now. Which one should be in the final annotation notes? We are going with the PECAAN ones since they are all imported into DNAMaster at once. Best, -Nick SCSU, New Haven CT |
Link to this post | posted 22 Feb, 2017 17:26 | |
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Thanks Chris – Yup, that was the issue! I'm not sure how it ended up locked, but it was indeed locked. Cheers, -Nick |
Link to this post | posted 22 Feb, 2017 16:29 | |
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My students are having a problem editing the Mabel genome in PECAAN, with the error stating that it is “Read-only", and thus cannot be edited/annotated. The same students can edit other SCSU genomes that have been added, but not Mabel. As an Admin, I have no problems editing Mabel. Any idea why there is a permissions error even thought they are approved Institutional Users? Best, -Nick |
Link to this post | posted 08 Feb, 2017 18:20 | |
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Hi Chris, We were attempting to perform the whole phamerated phage report for Flaverint, and it crashed on gp18. It seems to happen with the 2017VM Starterator, and the Github V1.1 version that I 'git cloned'. In fact, Starterator doesn't seem to like many of the A11's. Best, -Nick |
Link to this post | posted 06 Feb, 2017 22:20 | |
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Flaverint_Draft (A11) crashes at Gene 18 (Pham 8250) with the code below using the Starterator 1.1 from github. (I can however, get the Pham report from the WUSTL website.) Thanks, -Nick
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Link to this post | posted 22 Jan, 2017 15:41 | |
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Is the http://cobamide2.bio.pitt.edu/ server down (between Jan. 21nd-22nd, 2017)? The ftp server is not responding. I have tried CLI, several browsers and two operating systems to connect, and they all have failed. If it is not an error on my side, it would be nice if a message was posted somewhere (or an email to SEA-PHAGES faculty) that the server is down for regular maintenance, etc. |
Link to this post | posted 15 Dec, 2016 16:22 | |
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Awesome! Thanks Chris! |
Link to this post | posted 17 Nov, 2016 15:21 | |
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My students are having a very tough time getting a high enough yields with this new protocol! We may not make the deadline of tomorrow (11-18-16). We are following the protocol and keeping in mind all of the potential pitfalls with the kit. We have seen a little smearing on the "best" preps, and we have one prep that also does the disappearing trick after R.E. digestion. With the caveats of a NanoDrop in mind, we are getting ~40ng/uL to ~80ng/uL following the protocol, and in several cases when we did not split the one mL HTL (i.e. added 1mL of HTL to one column), the resulting yield was double (i.e. ~160ng/uL), which might be useful to know. Our lysate titers have been low as well, thus we have been working with lysates very close to 1x10^9 pfu/mL, because it has been the best that the students have been able to achieve this year (which is a separate issue to be sure.) Dan: With such great sequence coverage that has been seen from past years, would the contaminating host DNA really cause much of a problem with assembly? Maybe one could just add a bit of RNAse directly to the HTL's? It would be interesting to know if you have ever tried phage genomic sequencing with and without the addition of the DNAse/RNAse cocktail, and compared the assembly results. |
Link to this post | posted 15 Dec, 2015 15:14 | |
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Hello Anthony, This file has the instructions for the manual installation of Phamerator. We have done this before, and it worked fine. Best, -Nick |
Link to this post | posted 23 Nov, 2015 16:26 | |
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The "pham circle" tool is broken in Phamerator, and I believe that Steve C. is aware of this. In the meanwhile, if you can do some programming, Circos is an option to draw something similar. |