Link to this post | posted 12 Aug, 2021 20:05
byrumc@cofc.edu	Thanks, Dan! That helps! Christine

Link to this post | posted 12 Aug, 2021 20:05
byrumc@cofc.edu	Thanks, Dan! That helps! Christine

Link to this post | posted 12 Aug, 2021 19:11
byrumc@cofc.edu	Quick question…During assembly of the genomes, is there a program used to trim the reads or is there no need to trim the 150-bp single end reads before looking at them in Newbler? Thanks! Christine

Link to this post | posted 11 Jan, 2021 11:38
byrumc@cofc.edu	I have been running DNA Master using WINE on my Mac (High Sierra) since 2016 and have had no problems with it (including last week). When I tried to open it today, it wouldn't start at all. I downloaded Quartz and DNA Master again, but they still won't work. Has this method expired? I recently removed Flash Player from my computer. Would that cause a problem? Thanks. Christine

Link to this post | posted 16 May, 2020 22:13
byrumc@cofc.edu	Thanks so much for the feedback! That helps. I BLASTED again yesterday (before I got your note) and let it go all night, but it froze again. I closed that and then tried again this morning (Saturday…maybe there was less traffic). It took 9 hours, but it finally worked! Whew! I didn't know that the BLAST searches would continue after I quit DNA Master. Good to know. Thanks again! Christine

Link to this post | posted 16 May, 2020 03:18

byrumc@cofc.edu

I have been trying for several days to make the final DNA Master file after transferring the PECAAN txt file into the DNA Master Documentation section (on my Mac). I've tried to do this at least 7 times. First, I uploaded the FASTA file into DNA Master and then BLASTed all. After trying this twice I was able to get a file that had the BLAST results in it. I then went to the documents page in DNA Master and replaced that info with the PECAAN full annotation text file info (I selected all and replaced…I'm on my Mac, so I can't right click). That went well, but after adding the PECAAN info and parsing, all of my BLAST info disappeared. I cleared all BLAST data (just in case any was left)…and BLASTED again…it puts in the requests, but usually 0 results are read (sometimes it gets to 1 or 4 results read, but usually says 0 results read). It says Too many outstanding requests, attempting to retrieve results before initiating more queries. The the window disappears and there is nothing in the DNA Master file. All of the PECAAN info is gone, all of the predicted genes are gone and there is no BLAST information. I've been working on this for the last 2 days…trying slightly different approaches and the same thing keeps happening. I've never had this problem in the past. Is it because there are so many trying to submit their genomes right now and BLAST is overloaded? I've run the program at peak and non-peak hours. Any suggestions? Thanks for your help! Christine

Link to this post | posted 11 Sep, 2019 19:22
byrumc@cofc.edu	I was asking about multiple genes existing in different reading frames at the same time…based on the GeneMark(smeg) calls.

Link to this post | posted 11 Sep, 2019 19:22
byrumc@cofc.edu	I was asking about multiple genes existing in different reading frames at the same time…based on the GeneMark(smeg) calls.

Link to this post | posted 11 Sep, 2019 14:55
byrumc@cofc.edu	GeneMark(smeg)

Link to this post | posted 11 Sep, 2019 14:55
byrumc@cofc.edu	Hi Welkin, We're looking at LastJedi. I've attached the GeneMark(smog) output. Thanks! Christine 178Kb