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EELS-SI datasets were processed by the following procedure.
All datasets were processed by both PPP method and relative GPS method.
This choice is due to the general applications discussed here, where four different datasets were processed by the same algorithm.
The datasets were processed by an integrated strategy.
All ChIP-seq datasets were processed by first aligning sequence reads to the hg19 genome using Bowtie2 [ 55].
To analyze changes in molecular responses in individual cell types, the datasets were processed by comparing the transcriptome of each cell type in FW and SW conditions.
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Rules can also be defined to require that specific datasets be processed by specific workflow components (described further below).
The Pilot dataset was processed by fpocket and an all-against-all SiteHopper BSC was performed to create a matrix of binding site similarities.
First of all, there is only one robust placement of the diatom nuclear psb28 sequences in our analyses: when the dataset was processed by Bayesian analysis using advanced models CAT and CATBP, all the diatom nuclear and plastid psb28 sequences form short branches and cluster together, with posterior probabilities ranging from 0.77 and 0.98 for CAT and CATBP respectively (Figure 3).
The long-wavelength dataset was processed by the pipeline Xia2 [36] using 3D spot integration.
Each dataset was processed by deleting the genes with missing values to generate a complete data matrix, and the details of these datasets were listed in Table 1.
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