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  • thomasvangurp
    Member
    • Jan 2009
    • 12

    Hello from Thomas

    Hello there,
    I'm new here. I'm studying Biology at Wageningen University. Currently I'm working on a new idea for improving methylation sensitive AFLP (MSAP) using the complete Arabidopsis methylomes as published by Cokus et al and Lister et al. I've written some of my first algorithms that produce fasta-like files in which methylated cytosines are replaced by an 'X' and guanines opposite to a methylated crick strand 'C' replaced by a 'Y'. With those files i then perform in silico MSAP, for which I wrote a custom algorithm.

    If anyone is interested in this, had suggestions or questions about it, feel free to ask !

    Oh, and by the way, i should have studied bioinformatics. It's just amazing what you can do with a bit of programming :-)

    I'm curious what's happening around here, and hope I can contribute some day!

    Thomas

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  • GATTACAT
    Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by GATTACAT
    Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
    Yesterday, 11:43 AM
  • SEQadmin2
    Nine Things a Sample Prep Scientist Thinks About Before Sequencing
    by SEQadmin2


    I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

    Here are nine questions we think about, in roughly the order they matter, before...
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