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Next, we reconstructed trees using the pipeline described in [ 46].
Phylomes were reconstructed using the pipeline described in [ 82].
using the pipeline described in Segmentation of the Dataset.
New entries are automatically annotated and integrated into MethCancerDB using the pipeline described above.
The annotation was then loaded into the annotation database using the pipeline described above.
Data were pre-processed using the pipeline described in Touleimat and Tost [ 21], with additional modifications [ 21].
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We used the pipeline described in [12].
To call SNVs, we used the pipeline described in the section "Best practice Variant Detection with the GATK v4, for release 2.0" of the GATK webpage at http://www.broadinstitute.org/gatk/guide/.org/gatk/guide/
The obtained small RNAs were then classified and annotated using the bioinformatics pipeline described in the Materials and Methods.
Data from the spike array hybridization experiment were analyzed using the analysis pipeline described above for the heat shock experiments.
The data in [15] were analyzed using the same pipeline described above for our data; binding sites were identified using an adjusted p-value of 10−4.
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