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Forum: Illumina/Solexa 02-19-2018, 04:21 AM
Replies: 10
Views: 5,293
Posted By kerryp
my RTA failed less than 50 cycles into a 600...

my RTA failed less than 50 cycles into a 600 cycle MiSeq run. I've been in contact with tech support and they've agreed to replace reagents. BUT because it stopped so early on, could I re-use the...
Forum: Illumina/Solexa 10-19-2017, 08:02 AM
Replies: 2
Views: 1,228
Posted By kerryp
non-equimolar pooling to normalise read depth in libraries with different genome size

I'd like to sequence libraries of very different genome size on a single MiSeq run.

Eight bacterial samples with 4.5Mb genome size
One eukaryote sample with 23Mb genome size

Could I pool the...
Forum: Illumina/Solexa 10-19-2017, 05:48 AM
Replies: 2
Views: 1,143
Posted By kerryp
index diversity on MiSeq

Can I run 2-3 index combinations on MiSeq? I'd be using Nextera XT DNA sample preparation index kit and MiSeq v2 reagent kit. If I select index pairs with maximum diversity, might it be safe to try? ...
Forum: Illumina/Solexa 10-19-2017, 05:09 AM
Replies: 5
Views: 1,467
Posted By kerryp
Thanks - that's really helpful. I expect Illumina...

Thanks - that's really helpful. I expect Illumina don't communicate precisely what their transposon sites are? :)
I suppose it'd just be a case of prepping a couple of amplicons to see how it goes....
Forum: Illumina/Solexa 10-19-2017, 12:48 AM
Replies: 5
Views: 1,467
Posted By kerryp
Thanks nucacidhunter. Do you think I could prep a...

Thanks nucacidhunter. Do you think I could prep a 2kb amplicon (amplified from cDNA) using Nextera XT? Basically treating it like gDNA?
I usually run WGS with Nextera XT and MiSeq v2 reagent kit,...
Forum: Illumina/Solexa 10-18-2017, 08:41 AM
Replies: 5
Views: 1,467
Posted By kerryp
NexteraXT kit on cDNA amplicon?

Can I use the Nextera XT library prep kit on a 2kb cDNA amplicon? Just wanting to check that the tagmentation process will work ok on cDNA. I've only ever used it on gDNA for WGS.
Thanks in advance!
Forum: Sample Prep / Library Generation 10-05-2015, 08:03 AM
Replies: 15
Views: 15,166
Posted By kerryp
Thanks GenoMax

Thanks GenoMax
Forum: Sample Prep / Library Generation 10-05-2015, 07:07 AM
Replies: 15
Views: 15,166
Posted By kerryp
Haven't looked at the data beyond running it on...

Haven't looked at the data beyond running it on spades (where there seemed to decently few contigs). But when I ran the library on bioanalyser, the average fragment size for all samples were within...
Forum: Sample Prep / Library Generation 10-05-2015, 05:36 AM
Replies: 15
Views: 15,166
Posted By kerryp
thanks jessica_L Here's the charts screen - is...

thanks jessica_L
Here's the charts screen - is this what you were looking for?
Forum: Sample Prep / Library Generation 10-05-2015, 02:38 AM
Replies: 15
Views: 15,166
Posted By kerryp
are my phiX QC measures ok?

I've just used phiX (v3) for the first time on a miseq run. I was using the 500-cycle reagent kit (running 241*2 cycles), and using 1% PhiX.

According to my run summary:

aligned = 1.3%
error...
Forum: Illumina/Solexa 10-01-2015, 08:16 AM
Replies: 2
Views: 1,558
Posted By kerryp
Hi Jessica_L Thanks - yes, I see the...

Hi Jessica_L

Thanks - yes, I see the difference now between the library prep methods. We'll try the NEB kit and sonication and see how it compares with Nextera
Forum: Sample Prep / Library Generation 10-01-2015, 01:47 AM
Replies: 7
Views: 2,009
Posted By kerryp
We're doing small genome resequencing of...

We're doing small genome resequencing of bacterial genomes. We're not restricted to low inputs - we could use more DNA if needed
Forum: Illumina/Solexa 10-01-2015, 12:36 AM
Replies: 13
Views: 4,535
Posted By kerryp
Many (belated) thanks! :)

Many (belated) thanks! :)
Forum: Sample Prep / Library Generation 10-01-2015, 12:31 AM
Replies: 7
Views: 2,009
Posted By kerryp
Thanks nucacidhunter and kerplunk412 - is there...

Thanks nucacidhunter and kerplunk412 - is there any particular kit you'd recommend?

I can see us moving away from Nextera as we don't use their normalisation method any more (so we're just using...
Forum: Sample Prep / Library Generation 09-30-2015, 08:09 AM
Replies: 7
Views: 2,009
Posted By kerryp
library prep using sonicator - indexing

I'm currently using Nextera XT to prepare libraries for MiSeq. This involves 'tagmentation' which simultaneously fragments (enzymatically) and adds a tag sequence. We then amplify using Nextera XT...
Forum: Illumina/Solexa 09-30-2015, 07:14 AM
Replies: 2
Views: 1,558
Posted By kerryp
library prep using sonicator - indexing

I'm currently using Nextera XT to prepare libraries for MiSeq. This involves 'tagmentation' which simultaneously fragments (enzymatically) and adds a tag sequence. We then amplify using Nextera XT...
Forum: Illumina/Solexa 09-14-2015, 08:09 AM
Replies: 13
Views: 4,535
Posted By kerryp
running just one library on MiSeq (Nextera XT)

Just wondering how to go about running a single bacterial library (rather than multiple pooled bacterial libraries) on MiSeq. So far I'm only going from a post in a thread from a few years back,...
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