Real datasets for RISQ

This folder contains 8 files. They can be used to validate RNA-seq quantification tools and to make comparisons. The files "chr6.fa", "mm9chr6.gtf", "Read11.fa" and "Read22.fa" can be used for isoform quantification by different RNA-seq quantification tools. The files "chr1.fa", "chr2.fa","hg38_chr1.gtf","hg38_chr2.gtf", "file2.csv", "file3.csv" together with together with MAQC RNA-seq data (GEO Sample id: GSE83402) can be used to validate any new RNA-seq quantification tool with respect to qPCR data.
"chr1.fa" is human chromosome 1 sequence (Source: UCSC database).
"chr2.fa" is human chromosome 1 sequence (Source: UCSC database).
"chr6.fa" is mouse chromosome 6 sequence (Source: UCSC database).
"mm9chr6.gtf" is mouse chromosome 6 reference annotation with mm9 version (Source: UCSC database).
"hg38_chr1.gtf" is human chromosome 1 reference annotation with hg38 version (Source: ENSEMBL database).
"hg38_chr2.gtf" is human chromosome 2 reference annotation with hg38 version (Source: ENSEMBL database).
"Read11.fa" and "Read22.fa" are paired end reads generated from an RNA-seq experiment (Source Publication: https://genome.cshlp.org/content/early/2013/04/28/gr.146654.112.abstract).
"file2.csv" contains delta Ct values from qPCR experiment on same sample (Can also be downloaded from: https://www.nature.com/articles/s41598-017-01617-3).
"file3.csv" contains informations on which gene corresponds to which of the transcripts (Can also be downloaded from: https://www.nature.com/articles/s41598-017-01617-3).