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Thread | Thread Starter | Forum | Replies | Last Post |
Tech Summary: ABI's SOLiD (Seq. by Oligo Ligation/Detection), UPDATED for v2.0 | ECO | SOLiD | 67 | 04-23-2013 03:07 PM |
Tech Summary: Roche's 454 GS20 / FLX / Titanium | ECO | 454 Pyrosequencing | 12 | 09-11-2011 07:10 AM |
Tech Summary: Animated video explaining Helicos tSMS Next-gen Technology | apfejes | Helicos / Direct Genomics | 8 | 06-17-2011 10:10 AM |
problem withe Illumina solexa sequencing | g781 | Illumina/Solexa | 3 | 05-18-2010 10:05 AM |
In Sequence: With Summary Judgment in Hand, IP Suit Over SOLiD Tech Faces Trial in J | Newsbot! | SOLiD | 0 | 12-23-2008 01:53 PM |
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#41 |
Junior Member
Location: MGEL Join Date: Feb 2011
Posts: 4
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question... so paired end reads... are they from the same strand or the opposite??
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#42 |
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Location: Los Angeles Join Date: Feb 2011
Posts: 15
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Nobody ever answered the original question, so here goes:
The fluorescent bases are 3'-O-azido dNTPs with fluorophores linked to the bases. The azide group on the 3' O blocks addition of another nucleotide, and you can use a phosphine (TCEP) to chemically cleave the azide from the 3' O and allow the next nucleotide to be added. I believe TCEP also cleaves the fluorophore from the base. It's very clever, but unfortunately 3'-O-azido dNTPs are not available commercially. They would be fun to play with. |
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#43 |
Junior Member
Location: Vancouver, Canada Join Date: Jan 2011
Posts: 5
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Hi there,
I wanna do mRNA-seq on poplar, I review a bunch of literature without finding a single paper using pair-end sequencing, most of them use 454 sequencing. Does that mean pair-end sequencing does not work on poplar? Any suggestion? |
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#44 | |
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Location: Moscow Join Date: May 2010
Posts: 36
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What genome size? How many groups work on poplar sequencing? Best results for de novo assembly from 454, of course. But for resequencing why not use pair-end read? |
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#45 |
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Location: canada Join Date: Jul 2010
Posts: 15
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hi all,
Does anyone knows about illumina data downloadble from any published papers? many thanks |
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#46 |
Junior Member
Location: Colorado Join Date: Apr 2011
Posts: 1
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Can anyone explain how the RTA1.8 software identifies and locates clusters - is a particular nucleotide, e.g. an A and a C, required to be present in the first 4 or 5 base pairs of sequence? You can tell I'm a real newbie!
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#47 |
Junior Member
Location: Vancouver Join Date: May 2011
Posts: 1
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I am new to the whole NGS topic and I am going tot use Illumina sequencing. Does any one know how much library preparation is important? and does it worth to invest buying one of the preparation workstations?
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#48 |
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Location: uk Join Date: Mar 2009
Posts: 34
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Hi all,
Illumina has officially announced the updated specs for their Hiseq2000 and Hiseq1000 machines, with throughput up to 600GB. I've updated a google spreadsheet I keep with all the specs for all the companies that have commercial systems available here: https://spreadsheets.google.com/ccc?...WJleDRXaUhQTHc Please feel free to add more info to the spreadsheet if you have any more details. Cheers, Albert. |
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#49 |
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Location: Shanghai Join Date: May 2011
Posts: 15
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That's what I'm looking for. Thank you so much
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#50 |
Senior Member
Location: Boston area Join Date: Nov 2007
Posts: 747
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This is great!
A couple of questions. Are the HiSeq numbers per flowcell? Looking at the two HiSeq columns (1K & 2K), the data per run is 750M reads vs. 1000M (but if per flowcell, why different?) Looking at reagent cost, they are both at $12K/run BTw, shouldn't PacBio be more like 0.02M reads & .040 Gb for yield, not 2.94M reads & 2.94Gb yield (as I've stated publically, it's hard to really nail those numbers down for PacBio, but these are more likely in the right ballpark). Run time should probably be more like 0.08 as with the PGM. For PGM, should you have a column per chip? With the 314, the reads are somewhere in the 100K-200K per run. Also, perhaps it should be separated from the SOLiDs -- the projection you give for Q2 is obviously for the SOLiD family & a separate projection for the PGM (5X the number of reads & resultant increase in yield) could be appropriate. |
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#51 | |
Senior Member
Location: Boston area Join Date: Nov 2007
Posts: 747
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(if we ever start a FAQ, these would be obvious items to put there) |
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#52 |
Senior Member
Location: Boston area Join Date: Nov 2007
Posts: 747
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Search "novo AND transcriptome AND (illumina OR solexa)" -- that's currently 18 papers to get you started. Probably many more which just don't quite fit the search terms.
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#53 | |
Member
Location: Shanghai Join Date: May 2011
Posts: 15
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P.S. The first base ( and the next n bases) for imaging is from the adapter, is it necessary to remove such fragments in the fastq file generated by GA? |
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#54 |
Junior Member
Location: beijing Join Date: Jul 2011
Posts: 1
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It is very useful for us,thank you.This is my first post here.Hope that we could share our sequencing experiexce here.
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#55 | |
Junior Member
Location: Spain Join Date: Jul 2011
Posts: 1
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Hi,
This is my first post here.Thank you very much, this is very useful. Quote:
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#56 | |
Junior Member
Location: Penang Join Date: Aug 2011
Posts: 1
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#57 |
Junior Member
Location: Chengdu,China Join Date: Sep 2011
Posts: 2
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Thanks very much!
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#58 |
Junior Member
Location: earth Join Date: Jul 2011
Posts: 5
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Thanks, ECO, its useful for me, a beginner
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#59 |
Member
Location: Pune Join Date: Sep 2011
Posts: 14
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Nice Info.
__________________
Vaibhav Kulkarni |
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#60 |
Junior Member
Location: Italy Join Date: Dec 2011
Posts: 5
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Hi all,
I have Chip-Seq data by Solexa in three formats: 1) Sequence.bam 2) Sequence.txt 3) Export.txt What are the differences between these formats? |
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