This project contains the links to the datasets, software and code that was used for our study "Comprehensive analysis of RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues" (https://www.biorxiv.org/content/early/2017/06/12/053041)

ROP-project (beta version).  
Please expect frequent  updates.

Wrappers to run RNA-Seq aligners

Following Baruzzo et al. (2017), we have selected five RNA-Seq aligners that were reported to map a minimum of 75% of the reads simulated from human transcriptome using recommended parameters. For each of the RNA-Seq aligners we provide easy use wrappers with default and optomized parameters. The user is expected to install the tool of interest and downlaod the corresponding genome index. Before using, modify the following variable in the script : toolPath and index

• GSNAP (version 2017-09-30) run.GSNAP.sh
• HISAT2 (2.1.0) run.hisat2.sh run.hisat2.tuned.sh
• Novoalign (v3.05.01) run.Novoalign.sh run.Novoalign.tuned.sh
• TopHat2 (v2.1.1) run.tophat2.sh
• STAR (v2.5.3a) run.STAR.sh run.STAR.tuned.sh

Simulated RNA-Seq data

To demonstrate the accuracy of ROP’s read assignment, we simulated RNA-Seq data as a mixture of transcriptomic, repeat, immune, and microbial reads.

Fastq files of simulated data : mixture_reads_R1.fastq mixture_reads_R2.fastq

Mapped simulation reads are available here

Real SRA RNA-Seq data

FASTQ file are availabel here BAm file with mapped reads avaavailable here

TCRB-Seq data

We have used TCRB-Seq data prepared from three samples of kidney renal clear cell carcinoma (KIRC) by Li, Bo, et al. (2016) to demonstrate the assignment accuracy of immune reads. We downloaded matching RNA-Seq samples from the TCGA portal. In total, we obtained 301 million 2x50bp reads from three RNA-Seq samples. RNA-Seq FASTQ file are available here