Autarchy of the Private Cave

Tiny bits of bioinformatics, [web-]programming etc

    Archive for June, 2016

    The sugar conspiracy

    19th June 2016

    A long but interesting read: The Sugar Conspiracy.

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    Posted in Links, Misc, Science, Society | No Comments »

    How to: install Windows 7 on a recent laptop/PC from a bootable USB drive

    12th June 2016

    If you had ever seen the not-so-descriptive error message
    A required CD/DVD drive device driver is missing,
    then you have been trying to install Windows 7 (possibly using a bootable flash drive) on a recent laptop or desktop.

    There are two major obstacles for a somewhat-dated Windows 7 when it sees modern hardware:

    • USB 3.0
    • SSDs and newer disk drives in general

    Fortunately, both problems are easy to fix.
    Just follow the steps below; skip steps 1 and 2 if you already have a bootable Win7 flash drive.
    Read the rest of this entry »

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    TSW-friendly task and note management software

    5th June 2016

    A while ago I was looking for GTD/TSW-compatible android app.
    I ended up using Trello, Keep, and Calendar.

    But I always keep looking for new/improved tools, as right now I feel the best one does not exist…
    (If the best one can exist at all – requirements and conditions change all the time, so there is no fixed perfect immovable target.)

    I have been contemplating trying out the TSW methodology, but neither Keep nor Trello are quite there yet.
    I ended up using Evernote; after recent management changes and actually trying to become profitable it may as well last long enough.

    Everything was fine and calm until I have found workflowy yesterday.
    In essence, it is very similar to the text-file-based system that I have been using for at least half a year.

    Briefly, it is a web-based text editor on steroids, with possibly infinite nesting lists and seemingly full keyboard shortcuts control – no mouse needed.
    I recommend that you try the demo – it seems to be fully functional, and there is no need to sign up.

    This discovery made me read through pages and pages of this class of software tools.
    Here is a very brief summary of my findings: Read the rest of this entry »

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    Posted in Links, Misc, Notepad, Software | No Comments »

    Practical comparison of NGS adapter trimming tools

    1st June 2016

    I used to work with sequencing providers who were giving me fairly clean data.
    It was already barcode-separated, and had no over-represented adapter sequences.
    The only thing I had to do was to (optionally) quality-trim the reads, and check for biological contamination.

    Recently, however, I have come across some real-world data, which not only had contamination in it, but also quite a noticeable percentage of adapters.
    I did a quick test of multiple tools to see if they fit my requirements:

    • should be easy/logical to use: no arcane/convoluted command lines or config files
    • should detect adapters automatically, either using its own database or a provided plain FASTA file
    • should be reasonably fast
    • must leave no adapter traces behind: I prefer aggressive trimming

    I have tried the following tools:

    • fastq-mcf from the ea-tools package
    • skewer
    • TrimmomaticPE
    • cutadapt: haven’t used it directly, but it is used by some of the compared tools
    • bbduk from BBMAP
    • autoadapt
    • TrimGalore!

    Read the rest of this entry »

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    Posted in Bioinformatics | 2 Comments »