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The output alignment files in SAM format were further processed using SAMtools [ 43].
In a factorial design, the twenty family practices receiving the practice guidelines in the chart and computerised format were further randomly allocated to have risk presented during the consultation as AR or NNT (the seven "usual care" practices did not receive charts, thus were unable to participate in this part of the randomized trial).
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R-generated graphic files in portable document format (PDF) were further edited in Adobe Illustrator.
The structural MRI images were converted from the scanned images into the Analyze format, which were further processed using the Free Surfer software package (Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Harvard University, http://surfer.nmr.mgh.harvard.edu/).edu/
After initial analysis, the pivot formatted data were further analysed with the GeneSpring version 7 software (Silicon Genetics).
The resulting aligned reads in BAM format were analysed further by Cufflinks v2.0.2 [ 64] in several ways.
The FASTA formats of the sequences were further retrieved for analysis.
GO annotations were further formatted for input into the GOSlim program and the output was parsed to count the occurrence of each GO category.
Breast-related symptoms were reported in an open-ended format that was further categorized into pain, swelling, numbness, and miscellaneous symptoms.
This web interface is implemented using Java servlets which accept input queries, and hand them to the back-end RDB and then convert the results into a simple XML format which is further processed with XML stylesheets to yield the final HTML pages.
Individual Z-stacks were exported as 8-bit RGB TIFF formats and selected confocal Z-stacks were further reconstructed in Imaris (Bitplane, Zurich, Switzerland) as 3D models.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com