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Forum: Illumina/Solexa 09-27-2014, 12:23 AM
Replies: 3
Views: 1,341
Posted By WhiteSeal
Post What is a good run? Do you have a QC to determine that.

Alright, I was in a different thread and at one point the discussion went slightly of topic but it was clear to me that everyone had a different opinion on what is a good MiSeq/HiSeq run. So in a...
Forum: Illumina/Solexa 09-27-2014, 12:15 AM
Replies: 27
Views: 9,854
Posted By WhiteSeal
@Brian the image might not be too clear but it...

@Brian the image might not be too clear but it actually shows a boxplot of all the tile date (in this case 38 tiles) for each cycle.

@genomax data is indeed a de novo run.

I find it interesting...
Forum: Illumina/Solexa 09-26-2014, 06:46 AM
Replies: 27
Views: 9,854
Posted By WhiteSeal
@nucacidhunter: indexing was fine. 76 samples,...

@nucacidhunter: indexing was fine. 76 samples, barcode variation for each base was evenly distributed. So no issue there.

@GenoMax: I have not had the opportunity to look into the data myself,...
Forum: Illumina/Solexa 09-26-2014, 01:35 AM
Replies: 27
Views: 9,854
Posted By WhiteSeal
@GenoMax: samples were checked on BioAnalyzer to...

@GenoMax: samples were checked on BioAnalyzer to check the length of the fragments (all >700bp) so this should not happen. Also, we have seen this with almost all our 600PE v3 runs on the MiSeq.
...
Forum: Illumina/Solexa 09-25-2014, 06:08 AM
Replies: 27
Views: 9,854
Posted By WhiteSeal
We are seeing a lot of issues with these 600...

We are seeing a lot of issues with these 600 runs. There is a significant decrease in Qscores around 200 cycles (first read) and then around cycle 450 of the second read (a picture of %>Q30 is...
Forum: Sample Prep / Library Generation 09-24-2014, 07:07 AM
Replies: 8
Views: 5,894
Posted By WhiteSeal
Just on a different note, does everyone wash...

Just on a different note, does everyone wash their bead pellets while on the magnet? (I do btw)

I have read on the MinIon forum that someone was removing the samples off the magnet, then wash...
Forum: Sample Prep / Library Generation 09-24-2014, 06:56 AM
Replies: 9
Views: 3,584
Posted By WhiteSeal
In my current protocol we share our gDNA with the...

In my current protocol we share our gDNA with the covaris (duty cycle=10%,intensity=5.0, burst/sec=200, t=240sec, mode=frequency sweep) and we our getting good results. Without the shearing we also...
Forum: Sample Prep / Library Generation 09-12-2014, 05:47 AM
Replies: 8
Views: 5,894
Posted By WhiteSeal
We have been using AMPure XP beads for the...

We have been using AMPure XP beads for the Illumina TruSeq DNA/NANO/Amplicon prep for some time now and we always use 1.5ml LoBind tubes and dry them for 5 minutes in a heat block at 37celcius. With...
Forum: Sample Prep / Library Generation 07-23-2014, 03:44 AM
Replies: 9
Views: 3,584
Posted By WhiteSeal
Hi, I have been using the TruSeq DNA/TruSeq...

Hi,

I have been using the TruSeq DNA/TruSeq Nano kit on degraded FFPE material for quite some time now. For the FFPE material we use 150ng qubit measured DNA as input and we know from experience...
Forum: Sample Prep / Library Generation 11-29-2013, 04:03 AM
Replies: 20
Views: 13,561
Posted By WhiteSeal
I work with the illumina TruSeq DNA kit (with...

I work with the illumina TruSeq DNA kit (with gDNA to start with) and I have seen the double peaks (in all variations) a lot. Have done lots of samples on the HiSeq and some on the MiSeq as well, but...
Forum: Illumina/Solexa 11-06-2013, 06:54 AM
Replies: 2
Views: 3,353
Posted By WhiteSeal
Ah, that does make sense. I was confused by the...

Ah, that does make sense. I was confused by the 'Each CEP plate' line in the protocol, suggesting that there are two plates.

Maybe they should just have changed the line to 'Use a 200 μl single...
Forum: Illumina/Solexa 11-06-2013, 05:01 AM
Replies: 2
Views: 3,353
Posted By WhiteSeal
Question TruSeq Nano DNA sample prep

Hi Everyone,

I have done a number of TruSeq DNA preps, but now that it will be discontinued we have been looking into the TruSeq Nano prep. I have been reading the guide, but I found in the...
Forum: Bioinformatics 07-26-2013, 01:26 PM
Replies: 18
Views: 96,106
Posted By WhiteSeal
I would like to try the package for parsing...

I would like to try the package for parsing Interop files in well.. Did I read it correct that there is an R version?
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