SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tech Summary: Illumina's Solexa Sequencing Technology ECO Illumina/Solexa 73 05-26-2015 12:34 PM
Tech Summary: Roche's 454 GS20 / FLX / Titanium ECO 454 Pyrosequencing 12 09-11-2011 08:10 AM
Tech Summary: Animated video explaining Helicos tSMS Next-gen Technology apfejes Helicos / Direct Genomics 8 06-17-2011 11:10 AM
ABI SOLiD jsun529 Bioinformatics 1 08-20-2009 01:54 PM
In Sequence: With Summary Judgment in Hand, IP Suit Over SOLiD Tech Faces Trial in J Newsbot! SOLiD 0 12-23-2008 02:53 PM

Reply
 
Thread Tools
Old 12-29-2009, 06:36 PM   #41
snetmcom
Senior Member
 
Location: USA

Join Date: Oct 2008
Posts: 152
Default

Quote:
Originally Posted by deepak_bala View Post
Thanks for the reply. I was looking at it and maybe we can determine what the first base is with data from the primer 1 reads from primers n and (n-1).

Correct me if I am wrong, anyone.
the first base is given to you in your files, but AGAIN, you do not want to decode color space to read your sequence. Align your sequence in color space first.
snetmcom is offline   Reply With Quote
Old 12-29-2009, 06:42 PM   #42
deepak_bala
Junior Member
 
Location: USA

Join Date: Dec 2009
Posts: 7
Default

Quote:
Originally Posted by snetmcom View Post
the first base is given to you in your files, but AGAIN, you do not want to decode color space to read your sequence. Align your sequence in color space first.
Thanks for the pointer. I will.
deepak_bala is offline   Reply With Quote
Old 12-30-2009, 02:40 AM   #43
anago
Junior Member
 
Location: earth

Join Date: Nov 2009
Posts: 1
Default

Hi All,

back to the chemistry of SOLiD. With mate-paired libraries after the 'first mate' comes an internal adaptor. Do I think right that the 'second mate' is sequenced the same way but with primers matching with the internal adaptor?

Anago
anago is offline   Reply With Quote
Old 12-30-2009, 09:28 AM   #44
pmiguel
Senior Member
 
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,237
Default

Quote:
Originally Posted by anago View Post
Hi All,

back to the chemistry of SOLiD. With mate-paired libraries after the 'first mate' comes an internal adaptor. Do I think right that the 'second mate' is sequenced the same way but with primers matching with the internal adaptor?

Anago
Yes, the "R3" mate-pair reads are primed out of the internal adaptor.

--
Phillip
pmiguel is offline   Reply With Quote
Old 02-15-2010, 03:45 PM   #45
samanta
Senior Member
 
Location: Seattle

Join Date: Feb 2010
Posts: 109
Default Color space

Hello all,

I wrote this up on color space - nucleotide space conversion and added few Perl scripts to help you proceed.

http://www.homolog.us/blogs/?p=27

Please feel free to comment.

Manoj
samanta is offline   Reply With Quote
Old 07-06-2010, 09:27 PM   #46
lily Michelle
Junior Member
 
Location: suzhou

Join Date: Jul 2010
Posts: 1
Default

Hi all,

Is the flurosence attached to the base or the phosphate group?

thanks

lily
lily Michelle is offline   Reply With Quote
Old 07-06-2010, 10:10 PM   #47
genseq
Member
 
Location: Russia

Join Date: Dec 2007
Posts: 87
Default

Phosphate.
genseq is offline   Reply With Quote
Old 08-25-2010, 01:23 AM   #48
drambald
Junior Member
 
Location: Italy

Join Date: Aug 2010
Posts: 2
Default May be is a stupid question but...

Hello, I a the following question, regarding the use of AB Solid for ChIP-seq analysis.

To my understanding:

we tag a protein with an antibody, dismantle the cells, denaturate and sonicate the DNA, collect the fragments that were attached to the protein which was attached to the antibody and sequence them.

Problem is: the fragments from sonication should be 100-500 bp long, we only sequence 50 bases at each read: when and how does this further "reduction" take place ?

What should happen is:
1. The fragments are attached to beads
2. Amplification takes place on attached fragments
3. The bead ends up looking like an octopus with N copies of the same fragment
4. Those copies are actually sequenced, but due to technical limitations only the first 50 bases can be read

is this correct?

best regards
drambald is offline   Reply With Quote
Old 08-30-2010, 07:32 PM   #49
cmebai
Junior Member
 
Location: Heilongjiang China

Join Date: Aug 2010
Posts: 1
Default

Firstly ,thanks for your time of explaining the wonderful tech.And i have a problem ,that is :
At the step of primer reset is it the same strand to be sequenced ?
cmebai is offline   Reply With Quote
Old 08-30-2010, 07:55 PM   #50
snetmcom
Senior Member
 
Location: USA

Join Date: Oct 2008
Posts: 152
Default

Quote:
Originally Posted by cmebai View Post
Firstly ,thanks for your time of explaining the wonderful tech.And i have a problem ,that is :
At the step of primer reset is it the same strand to be sequenced ?
yes. there are 10,000's of copies of the strand on the bead. That is how the signal is detected.

but to simplify, the original strand is read at reset.

Last edited by snetmcom; 08-30-2010 at 07:56 PM. Reason: added
snetmcom is offline   Reply With Quote
Old 08-31-2010, 04:12 AM   #51
volks
Member
 
Location: hd.de

Join Date: Jun 2010
Posts: 81
Default

Quote:
Originally Posted by drambald View Post
4. Those copies are actually sequenced, but due to technical limitations only the first 50 bases can be read

is this correct?
sounds correct to me. have a look at these illustrations, i find them very informative:
http://seq.molbiol.ru/sch_lib_fr.html
http://seq.molbiol.ru/sch_clon_ampl.html
http://seq.molbiol.ru/sch_seq_ligase.html
volks is offline   Reply With Quote
Old 09-01-2010, 12:41 AM   #52
KevinLam
Senior Member
 
Location: SEA

Join Date: Nov 2009
Posts: 197
Default

Quote:
Originally Posted by volks View Post
sounds correct to me. have a look at these illustrations, i find them very informative:
http://seq.molbiol.ru/sch_lib_fr.html
http://seq.molbiol.ru/sch_clon_ampl.html
http://seq.molbiol.ru/sch_seq_ligase.html
Nice! Pity the tables look confusing without borders though..
KevinLam is offline   Reply With Quote
Old 10-11-2010, 01:29 AM   #53
holywoool
Member
 
Location: beijing China

Join Date: Sep 2010
Posts: 27
Default

hi,everyone!

It is said that we are able to detect sequence error when coping with reads in color space var di-base encode methord.And this is true.

But if a sequence error site has a high QUAL value,then can we make a conclusion that this is a sequence error site? If so,does it sound of some controdiction?

What I am confused is that whether we regardless its QUAL value while detecting sequence error ?

Thanks
holywoool is offline   Reply With Quote
Old 12-27-2010, 12:38 AM   #54
cpnine
Junior Member
 
Location: Seoul, Korea

Join Date: Dec 2010
Posts: 2
Default

eventually, I find it...
cpnine is offline   Reply With Quote
Old 01-14-2011, 04:52 AM   #55
laxsil
Junior Member
 
Location: norway

Join Date: Jan 2011
Posts: 1
Default

Hello!
am very new to the abi SOLId technology and am trying to understand things. Could anyone explain wat the bridge probes are?? And also the difference between degenerate bases and universal bases in the dibase probes

Last edited by laxsil; 01-14-2011 at 05:54 AM.
laxsil is offline   Reply With Quote
Old 04-13-2011, 08:42 AM   #56
analyst
Member
 
Location: US

Join Date: Jan 2011
Posts: 18
Default

Is it me or there is an error in the Fig. 5 under template sequence.

for possible dinucleotides for red color should be AT TA CG GC not TA TA CG GC

Since it is an image from ABI's document, the error is actually in the source.
analyst is offline   Reply With Quote
Old 11-03-2011, 10:23 PM   #57
navincish
Junior Member
 
Location: Ahmedabad, India

Join Date: Mar 2011
Posts: 1
Default Noise to signal ratio of SOLiD 4.0

N2S ratio of WFA more than 15% of the sample, is it suitable for sequencing run, however on the axis have very good intensity and in center of axis TXR fluorescence is slight increased.
navincish is offline   Reply With Quote
Old 12-22-2011, 08:35 AM   #58
doctortrout
Junior Member
 
Location: Colorado

Join Date: Dec 2011
Posts: 2
Cool Color scheme correction?

I am new to this next gen sequencing, so thanks for providing such a detailed and clear explanation. However, I found Fig. 5 confusing. I believe that a given fluorescent color needs to be assigned to dinucleotides that start with the same base (eg. AN = red) otherwise the sequence will have ambiguities. For example, if the sequence is AG, red would indicate AN. If you want to know N, then all dinucs starting with a G must have the same color (GN = one color, not red).
doctortrout is offline   Reply With Quote
Old 12-22-2011, 08:49 AM   #59
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

@doctortrout

I believe you have this reversed. If you assigned the same color to all dinucs that started off with the same base then you would be ambiguous. Assigning the same color to different starting bases prevents ambiguous assignments. Of course ideally there there would be 16 colors. But going with 4 colors then as an example let's say we have the sequence (R=>red, G=>green, B=>blue, Y=>yellow):

aRRGBGYY

With 'a' as the very starting base (we need to know this for color-space). We can then read this as bases:

aTACCATC


If 'Red' was assigned to all dinucs starting with an 'A'; e.g., AA, AC, AG, AT then we would read the colors as:

a???????

In other words what second base would the first Red indicate?

Color-space can be very powerful however I find it best for newbies to sit down and write down conversions from color-space to base-space and back in order to grasp the power.
westerman is offline   Reply With Quote
Old 12-22-2011, 09:25 AM   #60
doctortrout
Junior Member
 
Location: Colorado

Join Date: Dec 2011
Posts: 2
Default

This newbie will use the color sequence you entered is a good example of why the color scheme depicted in Fig 5 cannot be correct.

RRGBGYY can indicate either the base sequence you show: ATACCATC or the sequence CGCAACTC.
doctortrout is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO