RNAseqDB

To demonstrate how to run the pipeline, suppose we have a set of RNA-seq samples under a directory ~/data/RNA-seq/ and we want to quantify expression levels of genes in them. If samples are in SRA format, you should put them directly in ~/data/RNA-seq/. For FASTQ or BAM files, you should save each sample in a sub-directory under ~/data/RNA-seq/. The script will automatically find and analyze all the samples under the given directory ~/data/RNA-seq/. For samples downloaded from GTEx or TCGA, user should also put meta data file, SraRunTable.txt for GTEx and manifest.xml and summary.tsv for TCGA, under ~/data/RNA-seq/.