Forum: Sample Prep / Library Generation
11-25-2020, 06:06 AM
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Replies: 0
Views: 267
ATAC-seq nucleotide diversity?
Hi all,
I was wondering how is the expected nucleotide diversity of ATAC-seq libraries? If balanced I am thinking to include a test library in a MiSeq amplicon run as a means to increase the...
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Forum: Illumina/Solexa
11-25-2020, 05:47 AM
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Replies: 0
Views: 207
Too little PhiX - problem with denaturation?
Hi all,
first the TLDR:
Do you know of any factors that might cause PhiX denaturation to fail or reverse, outside of typical mistakes (NaOH concentration/pipetting mistakes/age)?
We have...
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Forum: Illumina/Solexa
08-24-2020, 04:20 AM
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Replies: 2
Views: 2,613
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Forum: Oxford Nanopore
08-24-2020, 03:39 AM
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Replies: 6
Views: 3,001
I recently did a couple MinION of runs with a...
I recently did a couple MinION of runs with a sequencing kit that was 6 days at room temp during shipment, before being stored beyond its expiration date due to the pandemic, with flow cells that...
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Forum: Sample Prep / Library Generation
05-28-2019, 02:45 AM
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Replies: 4
Views: 1,639
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Forum: Illumina/Solexa
10-13-2018, 09:22 AM
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Replies: 2
Views: 1,165
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Forum: Oxford Nanopore
09-26-2018, 03:59 AM
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Replies: 0
Views: 4,234
best approach in dealing with low input DNA
Hi everybody,
we already posted this in the Nanopore forums, but we wanted to have a better chance of receiving answers so we post it again here.
We are planning in our lab to perform an...
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Forum: Sample Prep / Library Generation
07-04-2018, 02:00 AM
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Replies: 5
Views: 2,143
Would anyone happen to have a pdf of this: ...
Would anyone happen to have a pdf of this:
GelStar nucleic acid gel stain: high sensitivity detection in gels.
White HW1, Vartak NB, Burland TG, Curtis FP, Kusukawa N. Biotechniques. 1999...
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Forum: Illumina/Solexa
06-25-2018, 03:04 AM
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Replies: 3
Views: 1,439
On further investigation I see that the pattern...
On further investigation I see that the pattern varies depending on the number of cycles in the sequencing kit, and also some variation among runs. It seems 2*150 cycles causes little or no sudden...
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Forum: Illumina/Solexa
06-19-2018, 10:32 AM
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Replies: 3
Views: 1,439
Base composition vs cycle, MiSeq vs HiSeq X
I have noticed that in our MiSeq runs we seems to always have an abrupt change in base composition in the last one or two cycles. The proportion of A goes to zero. Also I noticed we have a cyclic...
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Forum: Sample Prep / Library Generation
06-15-2018, 08:20 AM
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Replies: 5
Views: 2,143
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Forum: Sample Prep / Library Generation
06-14-2018, 04:46 AM
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Replies: 5
Views: 3,240
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Forum: Illumina/Solexa
03-01-2018, 04:11 AM
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Replies: 7
Views: 2,529
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Forum: Sample Prep / Library Generation
05-30-2017, 05:50 AM
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Replies: 12
Views: 8,542
Yesterday I experienced a similar problem, but...
Yesterday I experienced a similar problem, but the clumping (https://goo.gl/photos/rjZuhupF92WLqaeG9) happened in the first step, at the mixing of the bead solution and the DNA. This was HMW genomic...
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Forum: Sample Prep / Library Generation
11-11-2016, 08:58 AM
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Replies: 14
Views: 13,809
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Forum: Illumina/Solexa
11-05-2016, 07:42 AM
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Replies: 5
Views: 2,446
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Forum: Illumina/Solexa
11-04-2016, 07:10 AM
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Replies: 5
Views: 2,446
Thanks. Does this mean we should do a more...
Thanks. Does this mean we should do a more stringent size selection than the standard TruSeq two-sided magnetic bead size selection? Do you have any links to protocols for this? The Illumina Custom...
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Forum: Illumina/Solexa
11-04-2016, 06:26 AM
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Replies: 5
Views: 2,446
HiSeq X different insert size?
I am about to prepare TruSeq PCR-free libraries for HiSeq X sequencing.
From:
http://support.illumina.com/sequencing/sequencing_instruments/hiseq-x/questions.html
"The supported insert size on...
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Forum: Oxford Nanopore
10-11-2016, 02:02 AM
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Replies: 1
Views: 2,440
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Forum: Illumina/Solexa
08-30-2016, 09:21 AM
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Replies: 17
Views: 3,080
One way is to modify the sample sheet to use a...
One way is to modify the sample sheet to use a subset of the length of the indexes (at the cost of possibly increased false assignments). Typically the 8th base of Index1 and the 1st base of index2...
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Forum: Oxford Nanopore
07-29-2016, 05:48 AM
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Replies: 32
Views: 23,156
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Forum: Oxford Nanopore
07-26-2016, 09:33 AM
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Replies: 32
Views: 23,156
Thanks, this is very useful information.
We...
Thanks, this is very useful information.
We do have a bottle of Dynal M270 streptavidin beads, but it expired in 2012. I think the bottle has only been opened once, and it has always been stored...
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Forum: Oxford Nanopore
07-22-2016, 07:51 AM
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Replies: 32
Views: 23,156
Is it correct that the g-TUBES are optional? ...
Is it correct that the g-TUBES are optional?
Is the Hula mixer really necessary; can't we just mix by hand?
Could you suggest an alternative to the MyOne C1 Streptavidin beads? The smallest bottle...
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Forum: Oxford Nanopore
07-19-2016, 03:10 AM
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Replies: 32
Views: 23,156
MinION protocols?
Is there a site where I can find detailed protocols for library prep for MinION? A few days ago I signed up for the community, but I still don't have access to the community website. I would like to...
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Forum: Illumina/Solexa
07-19-2016, 02:58 AM
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Replies: 3
Views: 3,123
I suppose this is the two-step PCR approach? If...
I suppose this is the two-step PCR approach? If so you could also add a short secondary index between the specific primer and the tail, to make it "double-dual" indexing. With two pairs of tailed,...
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