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Recent Activity
All posts created by DanRussell
| Link to this post | posted 19 Jul, 2023 14:35 | |
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jcaoyao@gmail.com Hi, you can try opening a terminal and running this command: If that doesn't work, I'd suggest asking the internet! –Dan |
| Link to this post | posted 06 Jun, 2023 15:45 | |
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afreise Of course! Here you go: https://seaphages.org/forums/forum/222/ –Dan |
Posted in: Cluster-Specific Annotation Tips → Using This Forum
| Link to this post | posted 27 Jan, 2023 18:06 | |
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From Eric Miller: We are still recruiting undergraduates for the forthcoming summer 2023 REEU BeeMORE (Bees and Microbes) program at NC State University. Our goal is to recruit as many students underrepresented in agriculture and science as possible; our participants are selected based on their motivation to learn and to make the most of our 9 week program. Undergraduates in their second or third year are preferred, with most of them coming from outside the NC State University community. Here is the link to our home page: https://harvest.cals.ncsu.edu/beemore/ On the web page there is a recent video describing the program, a flyer suitable for printing or sharing electronically, and a link to the brief application procedure. We expect to keep the application window open for a bit longer. The program is funded for at least the next four years. Please share broadly! Thank you for helping get the word out, to your students and to your colleagues. Post it on one of your web pages citing summer opportunities! Thank you and all the best, Eric |
| Link to this post | posted 19 Jan, 2023 14:47 | |
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Hi Alison, Thanks. I asked because if they're the newer "M1" Macs, then we don't necessarily have a recommended way forward. (The chip architecture on the M1 Macs is different than the old Intel ones, and so VirtualBox will likely never work on M1s.) That said, if M1 is the issue, there's a big thread here on that: https://seaphages.org/forums/topic/5256/ –Dan |
| Link to this post | posted 18 Jan, 2023 16:29 | |
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Hi Alison, What kinds of computers do your students who are getting the error have? –Dan |
| Link to this post | posted 09 Nov, 2022 15:20 | |
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Hi Adam, 1. Yes, we use the standard Illumina protocol for denaturing/loading. The BioAnalyzer gives us numbers to adjust our starting pool to 4 nM. 2. Yes, we denature 5 µl of the 4nM pool. 3. We pool before we quantify, so we just take 5 µl of the pool. In your case, you'll need to pool libraries if you haven't done so. I'd recommend doing it in larger volumes than 0.25 µl though to avoid pipetting inaccuracy. If you've already normalized all the libraries @ 4 nM, then just take a microliter of each to make a 4nM pool, then take 5 µl out from that pool. (You should have plenty of extra library.) 4. We use the NEB Ultra II FS kit starting with 400 ng of input DNA. But other factors can determine final yield as well. For example, I think we only do 3 PCR cycles during the PCR step, but more cycles will get you more library in the end. Some libraries we've prepped are > 200 nM, others are only 5-10 nM. As long as you're above 4 nM, you should be fine. 5. Yes, we add between 3 and 6 µls of the phiX control before loading the sample. 6. Don't think so! Good luck, –Dan |
| Link to this post | posted 27 May, 2022 17:22 | |
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Hi Fernando, I'd recommend shooting for 100X coverage on your phage genomes. It might be a little higher or lower, but that's generally a decent target that's also not going to cost too much per phage. If you take an "average" phage genome of 70kb in length, that means you need ~7,000,000 bp of sequence to get to that coverage level. If the reads you're doing are 150 bases long, then: 7,000,000/150 = ~47,000 reads per genome Obviously that'll change depending on the size of the genome (often unknown!) and the length of the reads, so we usually shoot for ~100,000 reads per phage genome, though 50,000 will often be enough. As for protocols, we just use the standard protocol that comes with our library prep kit: https://www.neb.com/nebnext-ultra-ii-fns-dna/nebnext-ultra-ii-for-dna-library-prep After library prep, we use BioAnalyzer HS chips to check quantity/quality. Then the standard Illumina protocol to load the sequencer. We have a MiSeq, not a MiniSeq, so I don't have any specifics for the MiniSeq, but most of Illumina's sequencers these days are pretty easy to use. Take care and good luck! –Dan |
| Link to this post | posted 06 Apr, 2022 16:50 | |
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Hi Adam, Actually, they're not nearly nearly identical; there's only 32% amino acid identity between Arzan 58 and the next best match in the DB! (Which is Heisenberger 58 as of me writing this.) That's quite a lot of differences, and while it's probably reasonable to consider these homologs, they're still different enough that: 1. Phamerator's algorithm put them in different phams and 2. trying to make start calls on Arzan 58 based on Heisenberger 58 is not advisable. The AA sequences are 32% identical, but the nucleotide sequences show almost no similarity at all, so using a starterator report isn't a good idea in this situation, since SD sites and potential start codons have had lots of evolutionary time to change. This one you'll have to call on its own! –Dan |
Posted in: Annotation → Called an orpham but isn't?
| Link to this post | posted 01 Mar, 2022 17:34 | |
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uOttawaPHAGE Yes, we use that kit as called for in the protocol. uOttawaPHAGE Yep, those are the ones we use though we've never done more than 8 at a time. uOttawaPHAGE Haven't tried this. uOttawaPHAGE I honestly don't remember re: the starter pack, but in general you can ask for delayed ship dates on the Nanopore website if you don't want them to ship immediately. uOttawaPHAGE Yes, flow cells sort of have a "useful lifetime" in hours of sequencing. They usually say the flowcells can sequence for 72 hours. So you can stop after 4 hours, wash, and then do a different run later. But there's a substantial decline over time (both active sequencing time and sedentary fridge time)in the number of available pores, so you might have to sequence the second run for 12 hours to get the same amount of sequence as the first run got in 4 hours. A third run might need 48 hours. And so on. So you can't really look at that "72 hours" as like 6 equal 12-hour runs. There's also some carryover in barcodes from one run to the next. Though it's not a ton, it can be confounding if you don't have a ton of reads. Good luck! –Dan |
| Link to this post | posted 22 Feb, 2022 20:52 | |
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Hi SEA-PHAGES community, Phage-obsessed students who are about to graduate or who have recently graduated might be interested in this opportunity! It's a phage therapy research position at the FDA. https://www.zintellect.com/Opportunity/Details/FDA-CBER-2022-18 Good luck, –Dan |