| 20 Apr 2017 |
 candice | That’s great! The company is called Deep Science Ventures - here is their website: http://deepscienceventures.com/ | 10:14:39 |
 deb | thanks candice , will look into this as well - ideally looking for someone game to experiment with us | 10:26:17 |
| candice | Great, I will keep you guys in mind 🙂 | 10:44:48 |
 bioscisam | clare czechton just realised we do actually have snapgene still in our sponsor page since iGEM https://biohackspace.org/sponsors/ ... I think they should give us more free licences 🙂 | 12:45:41 |
| bioscisam | (we need use snapgene a bit during igem 2015 ) | 12:46:28 |
| bioscisam | although, proprietary software is not exactly in the spirit of things IMO | 12:48:39 |
| 21 Apr 2017 |
 oni | Eh up. Anyone know stuff about paired end reads in RNA-seq | 09:16:37 |
| oni | Trying to figure out whether or not the insert size vs the sequence matched size is good enough or not but a bit stuck | 09:17:22 |
| oni | Fastqc and samtools stats on a bunch of reads basically | 09:17:38 |
| oni | Also this is interesting : https://www.transcriptic.com/ | 09:59:24 |
| bioscisam changed their display name from samb1 to bioscisam. | 10:00:54 |
| bioscisam | transcriptic is seen them at the last couple of synbiobeta things .... defo a good idea... clouding your lab whatsits | 10:00:54 |
| oni | Am I right in thinking that if one has paired end reads, you'd want the insert size to be somewhat larger than the sequence being matched but not too much larger? | 10:09:06 |
| bioscisam | hmmm yeh paired ends are kind of confusing in RNA seq ... they sorta help you build scaffolds when you know what to expect in between the paired ends ... it's something I'm trying to fathom with the splicing analysis stuff I'm looking at | 10:27:00 |
| oni | Right... I don't understand why it should be so confusing though. I guess one paradox is that the literature says they are a known distance apart but it seems that separation changes a lot and besides, how would you really know? | 10:32:12 |
| bioscisam | it's useful if you have a reference .... so if you know what you're expecting to see | 10:39:03 |
| bioscisam | I'm still trying to understand how you work that into de novo methods | 10:39:19 |
| oni | I guess you'd just pattern match and overlap as best as you can | 10:53:07 |
| oni | de bruijin graphs appear somewhere along the line I believe | 10:53:19 |
| oni | 😕 | 10:53:20 |
| bioscisam | I thought paired ends helped more once you're trying to stitch contigs together ... de bruijns are where you build the initial assemblies from reads | 11:43:50 |
| bioscisam | although the stuff I'm learning about at the mo about how you go from de bruijn graphs to splicing graphs | 11:49:19 |
| bioscisam | umm I'm trying to refix this autoclave ... paniscus do you remember where the board mounted fuses go, what type they are? I can order some if we need more | 19:22:24 |
| bioscisam | !channel anyone else know about the fuses on the autoclave? 🙂 | 19:31:03 |
| bioscisam | also looks like the minion laptop is there in the lab on top of the fridge with a sign on saying "leave this running" but it looks like it isn't actually running and looks like the power is switched off at the wall where the laptop is plugged in | 21:52:35 |
| bioscisam | simon_hazelwood is that you ? I don't think your minion is running.. | 21:53:39 |
 jesuisldj | guyhanke: Oh wow that is a really useful tip!! thank you!! I might have some other questions, would you mind if I ask you about them? | 23:56:47 |
| 22 Apr 2017 |
 wzdd | What is minion? | 00:04:46 |
| wzdd | Also how did you go with the autoclave? | 00:04:59 |
| bioscisam | MinION nanpore thing | 00:05:23 |
