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Forum: Illumina/Solexa 05-02-2017, 05:28 PM
Replies: 0
Views: 441
Posted By ngseq
Unhappy Reduced coverage evenness of SureSelect QXT libraries with automation

Dear all,

We are trying to automate SureSelect QXT library prep with the Hamilton Star liquid handler, and encountered the issue of reduced coverage evenness. With automation, we had more...
Forum: Illumina/Solexa 01-09-2017, 05:56 PM
Replies: 113
Views: 19,663
Posted By ngseq
Novoseq-a terminator for ALL HiSeq platforms???

With Novaseq now on the market, who is still going to buy HiSeq 2500/3000/4000/X?
Forum: Academic/Non-Profit Jobs 06-06-2014, 06:51 PM
Replies: 0
Views: 1,623
Posted By ngseq
Whole Exome Sequencing Data Analyst/CHOP (updated)

You are welcome to send me a private message if interested in this position. Cheers! :D

Whole Exome Sequencing Data Analyst
The Children's Hospital of Philadelphia - Philadelphia, PA...
Forum: Academic/Non-Profit Jobs 05-29-2014, 01:46 PM
Replies: 0
Views: 1,753
Posted By ngseq
Whole Exome Sequencing Data Analyst-The Children's Hospital of Philadelphia

Requisition #: 13-30613
Job Title: Whole Exome Sequencing Data Analyst (The Children's Hospital of Philadelphia)
City: Philadelphia
State: Pennsylvania
Scheduled Shift: Days
Employee Type: ...
Forum: Illumina/Solexa 12-17-2012, 08:00 AM
Replies: 2
Views: 1,879
Posted By ngseq
1. In theory, you can. But it may be a problem to...

1. In theory, you can. But it may be a problem to isolate mtDNA with sufficient amount or purity for library prep in practice. It seems that most labs use long range PCR.

2. I don't know the...
Forum: Illumina/Solexa 12-10-2012, 01:50 PM
Replies: 0
Views: 1,065
Posted By ngseq
Smile duplicate reads removal for amplicon libraries?

Hi everyone,

Do you revove duplicate reads during data analysis if the library is an amplicon library or a raindance-captured library. My understanding is that there may seem to be a lot of...
Forum: Illumina/Solexa 09-27-2012, 10:10 AM
Replies: 0
Views: 911
Posted By ngseq
Creating custom reference genome from BED files?

Hi everyone,

I am wondering whether anyone has the experience of creating a custom reference genome from BED files. I hope to try MiSeq reporter for variant calling for a targeted sequence...
Forum: 454 Pyrosequencing 09-04-2012, 11:33 AM
Replies: 3
Views: 2,348
Posted By ngseq
Hi Benh, Thanks! You are probbaly right and...

Hi Benh,
Thanks! You are probbaly right and we'll try gel purification next time.
Forum: Core Facilities 04-06-2012, 11:02 AM
Replies: 11
Views: 8,692
Posted By ngseq
Thanks SWP. Looks like they do this for research...

Thanks SWP. Looks like they do this for research only according to their website.
Forum: Core Facilities 04-04-2012, 08:15 PM
Replies: 11
Views: 8,692
Posted By ngseq
CLIA certified HiSeq sequencing provider

Hi everyone,

Does anyone know any CLIA certified sequencing service provider? We hope to do exome sequencing for clinical diagnosis (SureSelect enrichment kit/HiSeq2000 preferred) so CLIA...
Forum: Ion Torrent 03-21-2012, 06:52 AM
Replies: 15
Views: 11,291
Posted By ngseq
thanks! looks like we should try to stick to...

thanks! looks like we should try to stick to 200nt kits.
Forum: Ion Torrent 03-17-2012, 05:30 PM
Replies: 15
Views: 11,291
Posted By ngseq
CCTT calling error

Wow, this would be very a big issue if proven to be a reproducible error for PGM. But given how many CCTTs there are in genomes (occuring once in every 256bp in totally random sequence) one would...
Forum: 454 Pyrosequencing 10-13-2011, 02:26 PM
Replies: 3
Views: 2,348
Posted By ngseq
Concatemer formation for RainDance library prep?

Hi All,

I am trying to make ligated libraries using the 454 Rapid library prep kit for DNA samples PCR amplified from RainDance merged primer/template droplets. After Ampure beads purification, I...
Forum: 454 Pyrosequencing 08-11-2011, 01:20 PM
Replies: 4
Views: 1,607
Posted By ngseq
Thanks RCJK. It is a shotgun ligated...

Thanks RCJK.

It is a shotgun ligated library.

here is what I got in the QualityFilterMetrics for the bad run (note control beads failed just as badly):

key ...
Forum: 454 Pyrosequencing 08-09-2011, 07:06 AM
Replies: 4
Views: 1,607
Posted By ngseq
Junior and Flx compatibility

Has anyone used Junior to sequence library made using GS FLX Titanium emPCR L kit? We tried doing so as our FLX sequencer is down but found only very few reads passed filter (even for control beads)....
Forum: 454 Pyrosequencing 08-01-2011, 01:02 PM
Replies: 2
Views: 863
Posted By ngseq
Thanks ajthomas!

Thanks ajthomas!
Forum: 454 Pyrosequencing 08-01-2011, 09:38 AM
Replies: 2
Views: 863
Posted By ngseq
Talking terminology of A/B for emPCR-A kits

Hi 454 users,

I've never used the emPCR kit for amplicon libraries before and get confused about the terminology of A/B for capture beads, amplification primers, enrichment primers and sequencing...
Forum: 454 Pyrosequencing 08-01-2011, 09:07 AM
Replies: 3
Views: 1,174
Posted By ngseq
hi Suefo, I've used both. We used 2cbp for...

hi Suefo,

I've used both. We used 2cbp for Junior and 3cpb for FLX (or ligated library in both cases) and it seemed to work well.
Forum: Introductions 03-18-2010, 03:18 PM
Replies: 0
Views: 736
Posted By ngseq
Talking hello

hello everyone,

i am very glad to find this website and it has been very helpful to me as someone new to next generation sequencing. thank you guys for posting!
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