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Forum: Sample Prep / Library Generation 12-21-2017, 11:26 AM
Replies: 8
Views: 1,251
Posted By BioKiwi
I wonder how many PCR cycles you have done and...

I wonder how many PCR cycles you have done and what was the total yield.
Forum: RNA Sequencing 11-12-2017, 04:55 PM
Replies: 5
Views: 1,574
Posted By BioKiwi
I wonder what brand of beads you have used for...

I wonder what brand of beads you have used for clean ups and if they have been used according to TruSeq protocol.
Forum: Pacific Biosciences 09-28-2017, 03:30 AM
Replies: 62
Views: 23,754
Posted By BioKiwi
One library, primer annealing, polymerase...

One library, primer annealing, polymerase binding, clean up and Magbead binding was done in one batch (one tube) then was splitted into three wells on the same sample plate and sequenced using the...
Forum: Pacific Biosciences 09-28-2017, 01:25 AM
Replies: 62
Views: 23,754
Posted By BioKiwi
We have found Sequel output to be inconsistent...

We have found Sequel output to be inconsistent and not sure if it is our machine. Just completed three SMRT cell runs with one library prepared for sequencing in bulk sequenced one after another but...
Forum: Pacific Biosciences 09-03-2017, 02:52 PM
Replies: 7
Views: 2,246
Posted By BioKiwi
Could anyone share their Sequel Run QC of a...

Could anyone share their Sequel Run QC of a Iso-seq library. PacBio does not seem keen to share details of what lies behinde their polished data.
Forum: Illumina/Solexa 06-06-2016, 08:20 PM
Replies: 13
Views: 3,644
Posted By BioKiwi
Thanks for reply Mike. I am not clear at the...

Thanks for reply Mike. I am not clear at the start of which read (R1, R2 or both) the inline barcode will be sequenced, if inline barcode is added to 5 end of forward primer. The structure of...
Forum: Illumina/Solexa 06-06-2016, 04:41 PM
Replies: 13
Views: 3,644
Posted By BioKiwi
Hi Mike I wonder using index+primer approach...

Hi Mike

I wonder using index+primer approach if index is sequenced at the start of red1 or R2.
Forum: Core Facilities 05-04-2016, 06:48 PM
Replies: 8
Views: 4,435
Posted By BioKiwi
Thanks Bukowski. Zephyr seems to be good for post...

Thanks Bukowski. Zephyr seems to be good for post PCR applications. I am looking to high end systems to have high throughput capability for future needs. Lab space is not an issue. Sciclone G3 NGSx...
Forum: Core Facilities 05-04-2016, 02:33 AM
Replies: 8
Views: 4,435
Posted By BioKiwi
Thumbs up Recommendation for illumina library prep automation

I wonder if anyone has experience or good knowledge of following NGS library prep (RNA-Seq, DNA and Agilent sequence capture) automation systems (pre-PCR) re their pros and cons to share. I am...
Forum: Sample Prep / Library Generation 04-17-2016, 11:06 PM
Replies: 10
Views: 2,666
Posted By BioKiwi
There is some anecdotal evidence that libraries...

There is some anecdotal evidence that libraries prepared with this kit in input range (250pg-10ng) do not show any correlation with 100 ng or higher input libraries prepared with the same input total...
Forum: Illumina/Solexa 07-23-2015, 07:21 PM
Replies: 2
Views: 3,546
Posted By BioKiwi
I am happy to have a look at references if anyone...

I am happy to have a look at references if anyone can recommend.
Forum: Illumina/Solexa 07-22-2015, 05:51 PM
Replies: 2
Views: 3,546
Posted By BioKiwi
How Illumina's kinetic exclusion amplification works

I wonder if anyone can explain how kinetic exclusion amplification used in patterned flow cells works. I have seen a youtube video but it does not explain the molecular mechanism of amplification or...
Forum: Bioinformatics 06-23-2015, 02:48 AM
Replies: 7
Views: 3,134
Posted By BioKiwi
Thank you very much everyone for your posts. I...

Thank you very much everyone for your posts. I have much clearer idea to plan my Honours project.
Forum: Bioinformatics 06-21-2015, 01:44 AM
Replies: 7
Views: 3,134
Posted By BioKiwi
Thanks for replies. I wonder if I can use similar...

Thanks for replies. I wonder if I can use similar approach for transcript isoform analysis.
Forum: Bioinformatics 06-19-2015, 02:16 AM
Replies: 7
Views: 3,134
Posted By BioKiwi
PacBio vs MinION

To compare PacBio long reads with MinION for de novo assembly of bacterial genomes what one should consider for library prep and assembly.
Forum: Illumina/Solexa 11-22-2014, 02:53 AM
Replies: 18
Views: 6,004
Posted By BioKiwi
Thanks for clarifying your position on PCR...

Thanks for clarifying your position on PCR contamination issues. I do not think that a mechanism or evidence has been provided for PCR contamination you have implied in earlier posts:

I was...
Forum: Illumina/Solexa 11-22-2014, 12:05 AM
Replies: 18
Views: 6,004
Posted By BioKiwi
If I understand you correctly, you are saying...

If I understand you correctly, you are saying that contamination by PCR is inevitable and nothing can be done about it. I have to disagree with you because PCR has been and is and probably will be...
Forum: Bioinformatics 09-30-2014, 01:06 PM
Replies: 4
Views: 827
Posted By BioKiwi
Thanks pmiguel. Is mapping to organnells genome...

Thanks pmiguel. Is mapping to organnells genome is a good option. I know that their size is smaller in comparison to nuclear genome, but they are available for some close relatives of the species.
Forum: Bioinformatics 09-29-2014, 11:27 PM
Replies: 4
Views: 827
Posted By BioKiwi
Mate pair distance calculation

Hi

I have two mate pair libraries with 2-3 kb and 6-8 kb inserts from a plant species. The libraries have been sequenced 2x100 cycles. FastQC shows good quality reads with low duplication levels....
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