BioXpress pipeline README

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BioXpress Downloader Step

Step 1 of the BioXpress pipeline

The downloader step will use sample sheets obtained from GDC Data Portal to download raw counts from RNA-Seq for Primary Tumor and Normal Tissue in all available TCGA Studies.

General Flow of Scripts

get_data_all_samples.sh -> get_hits_into_dir.py -> merge_files_tumor_and_normal.sh

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