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Solexa Pipeline documentation, or similar?

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  • Solexa Pipeline documentation, or similar?

    Hello everyone,

    I've been given the privilege to get to crunch trough our lab's first round of Solexa reads of small RNAs. I've worked on some earlier data, and plan on using MAQ for mapping, and perhaps CLCbios Genome Workbench, as soon as we get a license (expensive!!) - now, I need a little more information on the general Solexa Pipeline (quality scores, file formats (fastq vs. raw?), and so on) - are these documents in any way accessible publicly?

    Btw, thx for the great information I've found so far on this forum!

    Regards,
    JW,
    Uni. of Copenhagen, Denmark

  • #2
    Originally posted by jwaage View Post
    I've been given the privilege to get to crunch trough our lab's first round of Solexa reads of small RNAs. I've worked on some earlier data, and plan on using MAQ for mapping, and perhaps CLCbios Genome Workbench, as soon as we get a license (expensive!!) - now, I need a little more information on the general Solexa Pipeline (quality scores, file formats (fastq vs. raw?), and so on) - are these documents in any way accessible publicly?
    As far as I know the pipeline documentation isn't made available unless you own an instrument. They have been fairly good about giving people who don't have an instrument access to the software, I believe you need to register through iCom: http://icom.illumina.com/.

    I have a few little reports which might be of use, this one on how parts of the pipeline work:

    http://www.genographia.org/portal/to...eline.pdf/view

    and this one on next-gen stuff in general:

    http://www.genographia.org/portal/to...rimer.pdf/view

    People here are very helpful so I'd ask away.

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    • #3
      Those genographia links are dead now

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      • #4
        They are now online here:

        http://sgenomics.org/mediawiki/index.php/Genomics

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        • #5
          Cool

          I'm a puzzled about your PHRED/Solexa mapping table though. Isn't -5 taken as the lowest Solexa FASTQ score, thus while the log mapping does mean PHRED 1 would map to Solexa -5.87 (2dp), in practice it should be mapped to -5.0 (thus ASCII 59 ";" not ASCII 58 ":").

          Thanks

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