modencode blacklists with RNA-seq data?
On their page {https://sites.google.com/site/anshulkundaje/projects/blacklists} they say that these blacklists are applicable to functional genomic data based on short-read sequencing (20-100bp reads). These are not directly applicable to RNA-seq or any other transcriptome data types. Why id that so? In the differential expression analysis I performed recently with rna-seq data, I found a lot of significant fold changes that intersected with blacklisted regions. So should we remove them after all also in rna-seq?
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