Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
This is a sticky topic.
X
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • #46
    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, 06:56 PM. Reason: added

    Comment


    • #47
      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:


      Comment


      • #48
        Originally posted by volks View Post
        Nice! Pity the tables look confusing without borders though..
        http://kevin-gattaca.blogspot.com/

        Comment


        • #49
          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

          Comment


          • #50
            eventually, I find it...

            Comment


            • #51
              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, 05:54 AM.

              Comment


              • #52
                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.

                Comment


                • #53
                  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.

                  Comment


                  • #54
                    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).

                    Comment


                    • #55
                      @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.

                      Comment


                      • #56
                        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.

                        Comment


                        • #57
                          Originally posted by doctortrout View Post
                          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.
                          Not at all. The initial base *must* be an 'A' because that is what I defined it as. Once you have the initial base then the rest follows unambiguously. I gave you aRRGBGYY with the small 'a' representing the initial starting base of 'A'. I did not give you an unattached 'RRGBGYY'.

                          You have the correct underlying idea that color-space can be ambiguous if you start off with no-predefined starting base or if you go 'off-frame'. But when working with color-space you always either (1) start with a pre-defined base or (2) do mapping, in color-space, against a reference thus keeping yourself 'in-frame'.

                          The above is why everyone says "do work in color-space when you have color-space reads; do not translate into base-space as your initial step." See the many postings on SeqAnswers in regards to this.

                          Comment


                          • #58
                            I should point out that the very first dinuc in the columns under 'Template Sequence' in figure 5 is incorrect. It should be 'AT' instead of 'TA'. Looking at the '1st base vs. 2nd base' diagram to the left of 'Template Sequence' shows this.

                            Comment


                            • #59
                              Hi,
                              can you tell me why probes has 8 nucleotides? what´s a function of non-coding bases? thanks

                              Comment


                              • #60
                                ligase binding is most efficient at 8 bases. So you need 8mer probe.

                                Comment

                                Latest Articles

                                Collapse

                                • seqadmin
                                  Techniques and Challenges in Conservation Genomics
                                  by seqadmin



                                  The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                                  Avian Conservation
                                  Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                                  03-08-2024, 10:41 AM
                                • seqadmin
                                  The Impact of AI in Genomic Medicine
                                  by seqadmin



                                  Artificial intelligence (AI) has evolved from a futuristic vision to a mainstream technology, highlighted by the introduction of tools like OpenAI's ChatGPT and Google's Gemini. In recent years, AI has become increasingly integrated into the field of genomics. This integration has enabled new scientific discoveries while simultaneously raising important ethical questions1. Interviews with two researchers at the center of this intersection provide insightful perspectives into...
                                  02-26-2024, 02:07 PM

                                ad_right_rmr

                                Collapse

                                News

                                Collapse

                                Topics Statistics Last Post
                                Started by seqadmin, 03-14-2024, 06:13 AM
                                0 responses
                                34 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-08-2024, 08:03 AM
                                0 responses
                                72 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-07-2024, 08:13 AM
                                0 responses
                                81 views
                                0 likes
                                Last Post seqadmin  
                                Started by seqadmin, 03-06-2024, 09:51 AM
                                0 responses
                                68 views
                                0 likes
                                Last Post seqadmin  
                                Working...
                                X