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  • #1

    ENCODE RNA-Seq

    For a given list of genes, how can I query ENCODE for RNA-Seq data on a given cell type?
    I can obtain the graphical view in the ucsc genome browser for each gene, but I want to batch download the data for n genes in 1 cell type.
    Tx
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  • #2
    They haven't provided an automated way to do that. You would have to download the BAM files and count overlaps with genes manually. Note that the mapped data isn't very good, though. It is recommended to re-map with a newer aligner than what was used for the BAM files hosted in UCSC Browser.

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