I would like to obtain bigwig RNA-Seq coverage files for specific TCGA samples. Additionally, It would be great if I could download a specific locus from those bigwigs, and even average the coverage of multiple samples.
I believe this can all be achieved using the Recount2 Package, and associated packages in the QuickStart guide.
I simply cannot figure out how to download the TCGA bigwig files.
The download_study function in the recount QuickStart guide only explains how to download data using the SRA ID. I don't think TCGA has SRA IDs. If someone can help me get over the hump of importing the TCGA data as a RangedSummarizedExperiment simply by providing the TCGA ID, that would be great.
I don't know why I never got an email about your question despite the fact that you did use the recount tag. In any case, the answer lies in accessing the recount_url data.frame object provided by the recount package. You can subset it for TCGA and keep only the bigwig files, then use the resulting URLs. You might or mightnot want to download the mean_TCGA.bw file.