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Forum: Core Facilities 02-05-2020, 09:25 AM
Replies: 22
Views: 22,795
Posted By BrianJames
Hi ShyN, What ribo depletion are you using? ...

Hi ShyN,
What ribo depletion are you using? We've had good luck with the NEB reagent, and it is a pretty easy protocol. We've been using the EP motion for our polyA libraries with the NEB Ultra II...
Forum: Illumina/Solexa 08-09-2019, 09:26 AM
Replies: 2
Views: 3,889
Posted By BrianJames
Thank you for sharing. I've been looking for...

Thank you for sharing. I've been looking for something exactly like this!
Forum: Sample Prep / Library Generation 10-13-2016, 11:19 AM
Replies: 1
Views: 1,089
Posted By BrianJames
No experience with RIP-seq (yet), but it is a...

No experience with RIP-seq (yet), but it is a pretty fragmented starting material. I'm not sure you would get any more/better data from paired end sequencing.

Brian
Forum: Ion Torrent 05-29-2014, 11:45 AM
Replies: 12
Views: 10,598
Posted By BrianJames
Hi Brian, I think this is the link you want ...

Hi Brian,
I think this is the link you want http://seqanswers.com/forums/showthread.php?p=133568#post133568

Brian
Forum: Ion Torrent 02-18-2014, 07:52 AM
Replies: 19
Views: 6,944
Posted By BrianJames
I'm not sure what Ion Reporter uses, but the...

I'm not sure what Ion Reporter uses, but the torrent server uses TMAP to align reads.
Forum: Ion Torrent 02-16-2014, 10:58 AM
Replies: 12
Views: 10,598
Posted By BrianJames
You might want to take a look at this thread. ...

You might want to take a look at this thread.
http://seqanswers.com/forums/showthread.php?t=17678

I know I will look at it more when I get the chance. I must admit that I like Cuffdiff because...
Forum: Ion Torrent 02-15-2014, 08:30 PM
Replies: 12
Views: 10,598
Posted By BrianJames
I use Cuffdiff in cufflinks2. It's pretty...

I use Cuffdiff in cufflinks2. It's pretty straight forward, but I can see if I can find the command I ran on Tuesday, if you need it.
Brian
Forum: Ion Torrent 02-14-2014, 11:32 AM
Replies: 19
Views: 6,944
Posted By BrianJames
Yes, TS is the same as what is running your Ion...

Yes, TS is the same as what is running your Ion Proton.
Brian
Forum: Ion Torrent 02-14-2014, 11:14 AM
Replies: 12
Views: 10,598
Posted By BrianJames
There is a link a the Ion Community that...

There is a link a the Ion Community that describes a pipeline. You have to register, but it is free.

http://ioncommunity.lifetechnologies.com/docs/DOC-7062
It uses a combination of Bowtie2 and...
Forum: Ion Torrent 02-14-2014, 11:10 AM
Replies: 3
Views: 2,935
Posted By BrianJames
We have had ours since July of last year. We...

We have had ours since July of last year. We have mostly run AmpliSeq Exomes, and whole transcriptomes. Our last 20 or so runs have all been >10 Gb (with many in the 13-14 range), Q20 bases 8-11 Gb,...
Forum: Bioinformatics 09-19-2013, 08:53 AM
Replies: 4
Views: 3,933
Posted By BrianJames
OK. Are you working with DNA-seq, or RNA-seq? If...

OK. Are you working with DNA-seq, or RNA-seq? If it is DNA seq, I would be worried about not working in colorspace, if it is RNA-seq, removing duplicates from SOLiD short read data may not be a good...
Forum: Bioinformatics 09-18-2013, 01:42 PM
Replies: 4
Views: 3,933
Posted By BrianJames
I used to work with SOLiD data, and I have to ask...

I used to work with SOLiD data, and I have to ask why you are going to all of this trouble. In my experience, the best way to map SOLiD data is to stay in colorspace, and use Bfast, or mapreads...
Forum: Ion Torrent 07-26-2013, 03:30 PM
Replies: 22
Views: 27,611
Posted By BrianJames
I like your racks. How well did your 96 well...

I like your racks. How well did your 96 well plate setups work for .2 ml tubes? Are those the small rare earth magnets from the usual suspects (Harbor Freight, Grainger et al)?

Thanks,
Brian
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