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Hydra-Multi's read-pair clustering strategy is similar to that of Hydra and a detailed description of both the workflow (Supplementary Fig. S1) and algorithm can be found in the Supplementary Materials.
The chosen Oqtans tools were combined in a workflow (Supplementary Fig. S1).
Half of the SDS solubilized lysate was then used to typify the fiber by an electrophoretic procedure that allows separations of Myh isoforms, whereas the other half was processed for shotgun proteomics with an in-gel-based workflow (Supplementary Methods).
To better understand the evolutionary history of the six Musa NCED genes, a nucleotide sequence phylogenetic analysis was done using an in-house Galaxy workflow (Supplementary File 3 Figure S9).
Following a similar workflow (Supplementary Material, Fig. S1) as in our pilot paper (14), PTEN mutation-negative CS/CSL germline samples with elevated MnSOD levels (n = 608, including 10 pediatric patients; Supplementary Material, Table S2) were subjected to SDHB/ C/ D mutation analysis and their data compared with ancestry-matched controls (n = 700).
We now provide a new supplementary figure showing our workflow for converting from read counts to isoforms.
Users can apply the 'seq2pathway' function jointly, or in a two-step algorithm consisting of 'seq2gene' and 'gene2pathway' components separately (For workflow see Supplementary Fig. S1).
A flow chart describing the scheme of our workflow is provided (supplementary fig. S1, Supplementary Material online).
Supplementary File S3 Model application workflow for KNIME.
We provide our machine learning workflow as a supplementary KNIME archive file.
Supplementary Figure S1 shows the workflow of the feature-based classifier for somatic mutation prediction.
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