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Targeted whole-exome deep sequencing is now affordable for many academic labs and the multitude of studies underway is yielding datasets of unprecedented magnitude.
Two independent single-end cDNA libraries of sample A were constructed and sequenced, yielding datasets 'A' that contained ~29.7 million reads and 'A-rep' that was sequenced at 3-fold lower depth and contained ~9 million reads.
The datasets were down-sampled along the xy direction, yielding datasets that were 512 × 512 ×(100 200) voxels in size (voxel size of 0.2 μm × 0.2 μm × 0.2 μm), which improved the tracking and segmentation speed without losing accuracy and lowered the computer memory requirement.
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Units where fewer than six patients and/or fewer than three staff members responded to the questionnaires were systematically excluded from the secondary dataset analyzed, yielding a dataset comprising responses from 1909 patients and 929 staff members.
However, while these programs are useful, the resulting data often comprise presence records only, thus yielding unbalanced datasets (Crall et al. 2010).
Three different (0.25, 0.11 and 0.06) SNR of noises were used according to previous studies (Baxter et al., 2009), yielding three datasets with different levels of noises (Fig. 4A).
We created 10 replications with G=3, 5, 10 and L=50, 75 yielding 60 datasets.
The average read length for each of the three tissues was 99 bp, yielding complete datasets of 39.8 Gb for the head, 40.8 Gb thorax and 29.2 Gb for the abdomen.
After 2D classification, a large number of spurious particles as well as particles that show free polymerase or free clamp were removed, yielding a dataset of ∼90,000 particles.
Additionally, a search was performed within all gammaproteobacteria species, yielding a dataset comprising 100 gammaproteobacteria species (Additional file 4) and 200 universal gene families.
The raw data were filtered to remove adaptor reads, low quality reads, and reads of copy number = 1, yielding a dataset consisting of clean reads.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com