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ChIP-seq... Drosophila simulans... We subsampled reads from R2 ChIP-seq to 100x coverage using BBnorm (v37.54) with the parameters "threads=24 prefilter=t target=100", and created de novo contigs from the subsampled ChIPseq reads (ChIPtigs) with Spades v3.11.0 (-t 24 -careful –sc;).... Drosophila melanogaster... Drosophila... We created a custom Drosophila-specific consensus repeat library modified from RepBase v20150807 to include all complex satellite DNAs from Drosophila melanogaster.
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Expression profiling analysis: Transcriptome data from four biological replicates were generated using 8x15K Customized Drosophila Genome Oligo Microarrays (Agilent). Slide image data was quantified using Agilent's Feature Extraction software.... ChIP-Seq experiments were visualized as custom tracks using Integrative Genomics Viewer (Broad Institute). Total uniquely mapped tags were normalized to 10 million reads to generate tracks using HOMER.... Drosophila melanogaster
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