Link to this post | posted 27 Apr, 2016 01:03

lhughes

Greg - are you just trying to align with similar phage? You can do that pretty simply by creating a small database and using the web-based tool that was mentioned previously in the forum. You can also do a similar gene length alignment using DNA Master and the Genome Comparison tool with a few select phages for comparison. Would either of these accomplish you overall goal? Putting together a custom Phamerator database for all the phages is a pretty large job. Lee

Link to this post | posted 13 Apr, 2016 18:34
lhughes	There is a Chrome browser on the program menu in the VM (it is usually just above the Phamerator icon). Just open Chrome and use any web-based e-mail program to attach the file and e-mail it to your own e-mail address. Lee

Link to this post | posted 13 Apr, 2016 02:47
lhughes	Fastest way: E-mail it to yourself from inside the VM. There are other solutions, but that is the simplest. Lee

Link to this post | posted 07 Apr, 2016 03:38
lhughes	Thanks, Dan. I made the changes and everything works perfectly now. Lee

Link to this post | posted 06 Apr, 2016 19:27
lhughes	Chris: Thanks for the information. I tried everything you mentioned, but still no luck. I'm going to punt this one to Dan since I think he can resolve the issue quickly (and I think the answers to the sequencing questions are pretty straight forward just from a manual review). Lee

Link to this post | posted 05 Apr, 2016 20:40

lhughes

Ok - just got some Sanger reads back on a phage that needed some finishing. I am following Dan's button pushing document which says to do the following: "Adding Sanger Reads to a consed Assembly 1. Place the chromatogram (.ab1) files in the project’s chromat_dir. 2. Make a new file with the extension .fof (for file of filenames) and save it in the project’s edit_dir. This file should contain the exact names of the Sanger read files, one per line. 3. From the edit_dir, type consed and press Enter to launch consed. 4. In the Consed Main Window, click the Add New Reads button. 5. From the Files pane on the right, select your .fof file. 6. Click OK. 7. Once the process has finished, save the ace file." However, when I get to step 6 I get a "512" unknown error. Anybody have suggestions? Lee

Link to this post | posted 31 Mar, 2016 00:28
lhughes	Lee Hughes Was this problem ever resolved? I just tried running an auto-annotation and all I get back are tRNA calls and no protein-encoding genes. Lee Well - seemed to be working fine today. Don't know what changed. Lee

Link to this post | posted 29 Mar, 2016 18:12
lhughes	Was this problem ever resolved? I just tried running an auto-annotation and all I get back are tRNA calls and no protein-encoding genes. Lee

Link to this post | posted 23 Mar, 2016 01:37
lhughes	One of the files is likely corrupted. Open each individually and make sure they look fine (I've noticed that the gene graphics at the bottom of the DNA Master window are usually missing on corrupt files). Once you find the corrupt file, you'll have to get that student to send you a corrected file (they may need to go back to an earlier one before the error and remake the file). Lee

Link to this post | posted 08 Mar, 2016 20:43
lhughes	Thanks to Randy and his team for creating the tool and to Dan and Pitt for making a web-based version available. Had great success yesterday with setting up a database for my Streptomyces phages and was able to use the data to create a Splitstree output. This is something that's been on my to-do list for a while, so very happy to be able to do it now! Lee