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Tech Summary: ABI's SOLiD (Seq. by Oligo Ligation/Detection), UPDATED for v2.0

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  • #61
    SOLiD quality data box-plots.... strange?

    hi everyone,
    I have used the SOLiD2std.pl to change the csfasta and qual files to standard fastq files.
    I then ran fastqc to view boxplots of quality data and got these results, attached.
    They seem to have poor quality every 5 nt, as if the primer 5 of the procedure failed....
    Has anyone seen this type of quality plots before???
    I am new with solid data, have worked with ilumina and 454 before.
    Thanks for any guidance in advance.
    cheers
    maximo
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    • #62
      which adapter to start sequencing, P1 or P2 primer?

      Hi,

      I'm using SOLiD SAGE. The SAGE method seems to preserve the strand information. The only unclear question is which primer (or adapter) SOLiD uses to start the sequence. According to the chemistry, it is likely the P1 primer and reading from 3' to 5'. Can anyone confirm it?
      I stuck with this for a long time, hopefully someone can have an answer,

      Thanks so much,
      Hoa

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      • #63
        Hi!

        I'm analyzing a "second-hand" dataset generated using SOLiD 4. It is a transcriptome mate pair library that is 52 x 37 nt, and I cannot for the sake of me find the protocol that was used to generate those specific read lengths. I have F3 and R3 reads, so I am assuming it is a circularization protocol, but I do not know what the size selection parameters were, or how the circles were cut to produce the final fragments. This info would be very valuable for a more accurate mapping.

        Any knowledge would be greatly appreciated!

        Thanks a lot,

        Carmen

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        • #64
          SOLiD

          please i want to know which base shall i know to begin translating the colours to base sequence?

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