Link to this post | posted 22 Jan, 2016 05:21
lhughes	Well - looks like my issue is something different (attached). At least it still loads for me. Sorry if that wasn't any help. Lee 213Kb

Link to this post | posted 21 Jan, 2016 14:59
lhughes	I'll have to try to check when I get home, but I have a problem with my desktop at home that gives an error message when I try to start the VM (not sure if it is the same message as the one you showed). After I get the error, I just close the error box by clicking OK and then hit start again. The VM starts just fine after that.

Link to this post | posted 21 Jan, 2016 14:55
lhughes	Thanks for setting this up, Tammy. My students with Mac's were able to successfully install the program. Very helpful since in the past we just focused on the PC laptops and made the others use the lab computers. Now almost everyone can use their own. Lee

Link to this post | posted 08 Nov, 2015 03:03
lhughes	Figured it out! I was using the old form, not the newer form of the command (forgot to read the comments at the bottom of the video).

Link to this post | posted 07 Nov, 2015 21:08
lhughes	I have tried to add Illumina reads to an assembly using "addSolexaReads.perl" and following Dan's instructions. However I keep getting the following error "-ace must be specified". Everything looks correct to me with the command and filenames. Any suggestions? Lee

Link to this post | posted 07 Nov, 2015 02:11
lhughes	Joe: On your original question (in case you end up using the older procedure), I have found that switching the order so that you dissolve the PEG first (slow additions until completely dissolved), then slowly add small amounts of NaCl, that I can get it to dissolve completely without heating. It just takes time. I've never had any luck dissolving the salt first and then the PEG. Lee

Link to this post | posted 22 Oct, 2015 21:23
lhughes	Chris - I am having trouble with Yara_Draft. I've done all the troubleshooting that you list on the "sticky" note in the other topic, but it still crashes at Pham 117 of 135 each time I run it. Lee

Link to this post | posted 22 Oct, 2015 19:37
lhughes	I just wanted to express my happiness to see that a new episode of "Sounds of the Sea" was released. I really enjoy the discussions of phage biology that are in those each time. Lee

Link to this post | posted 17 Sep, 2015 00:50

lhughes

It does seem that this method primarily works with those that sporulate in liquid media. So far we've had great success with S. griseus and S. venezuelae using the spread plates. Others are not so easy to do. I think we've tried S. albus this way and have had trouble getting phage. I am pretty sure my student has switched back to spores on that one (he had a few positives, but lost them early in the process so he's trying again). It is definitely much easier to do these plates and avoid the whole top agar issue. Chris - We haven't tried that particular method, but does seem like it would be faster than waiting for the incubation step as long as you get good infection. Lee

Link to this post | posted 16 Sep, 2015 16:52

lhughes

Hi All: Bekah - we've been using spread plates with liquid cultures of Streptomyces instead of the spore/top agar method at UNT. Steve got his protocols from me, so I'm to blame I sent him the following information by e-mail this morning about how we get good lawns with this method: We usually grow up 50 mL culture until turbid (for a subculture usually 2 days, for an initial culture from spores usually 4 days). Then we centrifuge in a 50 mL conical at 3000rpm (Sorvall tabletop with buckets), pour off all but about 10 mL of the supernatant, and resuspend. 100 uL of this usually gives a nice confluent lawn. Lee