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ShortStack Tutorial now available

3/18/2013

 
Today, I released a full Tutorial on using ShortStack, complete with step-by-step instructions and a full set of sample data.  The tutorial is at http://axtelldata.bio.psu.edu/data/ShortStack_TestData/.  In addition, a new ShortStack version was released (0.4.2), which is simply an update to the README documentation to reflect the new tutorial data.  The tutorial should make it easier for users to begin using ShortStack productively in their work. Finally, I'm happy to report that a manuscript describing ShortStack and its performance in seven species (four plants, three animals), has been accepted for publication in the journal RNA.

As always, comments and bug reports welcome. -- Mike Axtell

ShortStack 0.4.0 Released

12/27/2012

 
ShortStack 0.4.0 has been released.  This is a major update which offers substantial speed improvements relative to previous versions.  The speed improvements are due primarily to a new filtering method that reduces the number of RNALfold calls.  Previously, all small RNA clusters were subjected to RNALfolding (except those that were too long -- see documentation).  In this new release, highly repetitive clusters, and those that are not dominated by small RNAs in the acceptable size range (in other words, have DicerCall of "N") are not eligible for secondary structure analysis.

The filtering by repetitiveness is accomplished using a metric I am calling the "Uniqueness Index" (or "UI" for short).  The UI is the ratio of repeat-normalized abundance / total mappings at a locus.  For highly repetitive loci, where most mappings come from reads that are highly multi-mapped, the UI approaches 0.  In contrast, for very unique loci, where most to all of the mappings are from reads that are uniquely mapped at the locus, the UI approaches or achieves a value of 1.  By default, ShortStack will not attempt RNA folding for any locus with a UI of less than 0.1.  This setting is adjustable with the new parameter --minUI.

This should offer substantial speed improvements, especially for large highly repetitive plant genomes which spawn 

ShortStack updates

10/18/2012

 
Posted update to 0.2.3 today, which fixes an error in the formatting of the BED files ... in all older versions the blockStarts field (column 12 of the bed line) was incorrectly reported in 1-based coordinates.  With this fix, blockStarts are now correctly listed in zero-based coordinates per the BED specification.

Also note that I am working on a major new release, version 0.3.0, which will incorporate (at a minimum) the following new features:

1. The ability to provide a "flag-file" of coordinates corresponding to known elements of interest (e.g. repeats, mRNAs) or for flagging for exclusion (e.g. tRNAs, rRNAs, etc).  The results file will flag small RNA clusters that overlap one or more of the loci in the flag-file.  This will be useful for quality control, for instance in easily identifying clusters that are rRNA fragments or tRNA fragments, for instance.
2. Preset switches for animal vs. plant MIRNAs, which should enable bett

ShortStack 0.2.0 released

8/29/2012

 
Major update in this release.  Most significant change is a major improvement in the accuracy of calling hairpin-derived, but not miRNA, loci.  Many fewer false positives / borderline cases are called by this new release, while annotation of longer hairpins (e.g. loci like Arabidopsis IR71) is much improved.  See the ShortStack page.

ShortStack version 0.1.4 released

6/28/2012

 
New release is here.  Changes:

1) Prep_bam.pl helper script updated
    to deal with .sam lines corresponding to unmapped reads without
    breaking. This also enables "one-step" mapping and .bam file preparation
    using bowtie (see 'Quick Start' section below).

2) ShortStack.pl also
    updated to prevent breaking upon encountering .sam lines corresponding
    to unmapped reads.

3) Coloring of .bed files now dynamically adjusts to
    make a nice 'rainbow' (from red through green to blue) regardless of the
    size of the dicer range.

4) Finally, an additional filter was added to
    prevent excessive splitting of initial de-novo clusters into
    hairpin-associated clusters ... initial clusters are now prevented from
    splitting if they would spawn more than --maxsplit child hairpins
    (default, 3). This prevents inappropriate splitting of very large
    clusters that might harbor a number of sub-optimal hairpins.

    -- THIS WEBSITE HAS BEEN REPLACED ... please go to http://sites.psu.edu/axtell for the current Axtell Lab Website! --

    Author

    Michael Axtell, lab PI
    Associate Professor
    Biology Deprtment
    Penn State University

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