The created dta files were then merged using the merge script tool from Matrix Science (http://www.matrixscience.com).com
When Arabidopsis (sd = 15) calls were filtered through the merge script, total calls were reduced by as much as 70% (average 61%) with recall diminished, on average, 27%.
In addition, a merge script has been added which will filter and rank calls providing researchers with an accurate and condensed set of calls curated from all the tools.
We then generated an assembly across all individuals for that species using Trinity r2012-01-25 [ 43], and then removed redundancy across these assemblies using a custom merge script using blat, cd-hit-est, and cap3 [ 44- 46].
In SV-AUTOPILOT, a merging script was developed to take all the calls, filter them, and provide a merged output (provided in Additional file 1).
As shown in Figure 4, the merging script is able to cluster calls by evaluating their breakpoints relative to the tool algorithm type applied (see methods section for a complete description).
We have packaged several of these tools into a single Virtual Machine pipeline, SV-AUTOPILOT, to facilitate reproducible research and coupled that with a powerful merging script that filters and ranks calls providing researchers with an accurate dataset on which to begin their bench validations.
After annotation, tables coming from GIN are used as input for a set of custom scripts (merge, PIES_PEAKS_GD, TSS_3UTR_dist) aimed at generating a tabular annotation of the enriched regions as well as annotation plots (pies showing genomic distributions and density plots of the peaks surrounding TSS and 3'UTR).
But she wisely merges her script with the "living newspaper" concept, using the clown and the voice-over to tease the audience out of its passive state.
Peak lists (in PKL format) from the analysis of all 12 digested gel bands representing a single sample were concatenated using the Perl script merge.pl (http://www.matrixscience.com) and exported in MGF format.
