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Forum: Illumina/Solexa 10-04-2017, 07:01 PM
Replies: 26
Views: 6,258
Posted By nangel
NovaSeq Experience

Hi, I have seen a lot of the theoretical discussion around the NovaSeq and the resulting data. I was just wondering if there were any users that were actually running a NovaSeq that could comment on...
Forum: General 10-26-2015, 02:20 PM
Replies: 1
Views: 1,039
Posted By nangel
Commercially Available Mixed Bacterial Mock gDNA Wanted

Does anyone know of a commercially available mixed bacterial mock gDNA that is available. We use mixed mock as our internal positive control in each amplicon run and would like to purchase this...
Forum: Illumina/Solexa 10-25-2015, 08:24 PM
Replies: 5
Views: 2,402
Posted By nangel
Low Diversity Libraries on NextSeq

Has anyone run low diversity libraries on the NextSeq500? Can you compensate with a certain amount of PhiX or is it still better to run the libraries through the MiSeq multiple times to get the read...
Forum: Illumina/Solexa 05-05-2015, 05:18 PM
Replies: 16
Views: 4,864
Posted By nangel
We only run our amplicons at 800 or below...

We only run our amplicons at 800 or below clustering with at least 10% PhiX. The recent decline in R2 quality has been confirmed by our FAS as a problem world wide with some batches of 2 x 250 bp...
Forum: Illumina/Solexa 05-03-2015, 02:56 PM
Replies: 16
Views: 4,864
Posted By nangel
We didn't see a huge improvement after the bleach...

We didn't see a huge improvement after the bleach washes or using another machine that should not have been affected by fungal contamination. I think our issue is something different after all. As...
Forum: Illumina/Solexa 04-21-2015, 03:32 PM
Replies: 16
Views: 4,864
Posted By nangel
We are also doing the full line wash with bleach....

We are also doing the full line wash with bleach. My concern was that on going back to review all of the amplicon runs on the machine the pre-phasing and error rate were in exactly the same range...
Forum: Illumina/Solexa 04-20-2015, 03:23 PM
Replies: 16
Views: 4,864
Posted By nangel
Hi, we had noticed a similar fungal like growth...

Hi, we had noticed a similar fungal like growth on the side of the bottle containing the sipper after we had the machine in stand by for a few weeks. Although, I swapped all the solutions over before...
Forum: Illumina/Solexa 04-19-2015, 05:23 PM
Replies: 6
Views: 1,858
Posted By nangel
XT kit uses much less DNA but this means that...

XT kit uses much less DNA but this means that there are slightly more PCR steps in the protocol (but only 12 so it's not terribly drastic)- that might be a consideration, if you had the available DNA...
Forum: Illumina/Solexa 04-19-2015, 04:40 PM
Replies: 6
Views: 1,858
Posted By nangel
Hi. We have also made the move over from 454 to...

Hi. We have also made the move over from 454 to Illumina and have environmental samples that often have limited DNA available. We have made successful libraries using the following DNA: Nextera XT...
Forum: Sample Prep / Library Generation 03-31-2015, 01:02 PM
Replies: 3
Views: 1,947
Posted By nangel
If you were just running the 12 16S samples then...

If you were just running the 12 16S samples then you would need to use PhiX to provide enough diversity in the sample (usually 10% or higher). Using your metagenomic library will provide that...
Forum: Sample Prep / Library Generation 03-30-2015, 07:16 PM
Replies: 3
Views: 1,947
Posted By nangel
Yes, using this kit for 12 16S amplicon samples...

Yes, using this kit for 12 16S amplicon samples will be a massive overkill. Even with 192 samples per run you get far more reads than you really need. If you have metagenomic samples that you were...
Forum: Illumina/Solexa 02-26-2015, 01:13 PM
Replies: 12
Views: 9,780
Posted By nangel
We routinely use 27F primer for Miseq...

We routinely use 27F primer for Miseq (AGAGTTTGATCMTGGCTCAG). Haven't had any issues when compared to other primer sets that we have in use. When you say that your runs didn't succeed is it in...
Forum: Sample Prep / Library Generation 12-02-2014, 04:45 PM
Replies: 0
Views: 1,353
Posted By nangel
Automation platform for Library Prep-help needed

Hi, We are currently moving our amplicon sequencing library prep over to an automatic platform. Before outlaying for machinery and programming, can anyone advise of positive or negative experiences...
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