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  • holywoool
    replied
    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

    Leave a comment:


  • KevinLam
    replied
    Originally posted by volks View Post
    Nice! Pity the tables look confusing without borders though..

    Leave a comment:


  • volks
    replied
    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:


    Leave a comment:


  • snetmcom
    replied
    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

    Leave a comment:


  • cmebai
    replied
    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 ?

    Leave a comment:


  • drambald
    replied
    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

    Leave a comment:


  • lily Michelle
    replied
    Hi all,

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

    thanks

    lily

    Leave a comment:


  • samanta
    replied
    Color space

    Hello all,

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



    Please feel free to comment.

    Manoj

    Leave a comment:


  • pmiguel
    replied
    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

    Leave a comment:


  • anago
    replied
    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

    Leave a comment:


  • deepak_bala
    replied
    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.

    Leave a comment:


  • snetmcom
    replied
    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.

    Leave a comment:


  • deepak_bala
    replied
    Originally posted by ECO View Post
    You're right, and you do know the first base based on the adapter/primer you use. I'm sure someone will chime in soon with a more detailed answer....
    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.

    Leave a comment:


  • ECO
    replied
    Originally posted by deepak_bala View Post
    Hey guys, I need a clarification about the two-base encoding (should be called 'decoding'!). Maybe I haven't understood correctly, but we need to know the first base to be able to decode correctly, right? I am not clear how one would decide/know what base comes first, 'cos I think it is critical to decoding the sequence.

    Thanks for any help!
    You're right, and you do know the first base based on the adapter/primer you use. I'm sure someone will chime in soon with a more detailed answer....

    Leave a comment:


  • deepak_bala
    replied
    Hey guys, I need a clarification about the two-base encoding (should be called 'decoding'!). Maybe I haven't understood correctly, but we need to know the first base to be able to decode correctly, right? I am not clear how one would decide/know what base comes first, 'cos I think it is critical to decoding the sequence.

    Thanks for any help!

    Leave a comment:

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