Kevin Hsieh edited this page Aug 13, 2018 · 178 revisions

ROP : Read Origin Protocol

WARNING: This wiki is outdated. Please refer to https://github.com/smangul1/rop for the latest information about using ROP.

Quick Start

ROP discovers the source of unmapped reads, which originated from complex RNA molecules, recombinant B and T cell receptors and microbial communities.

Download ROP using

git clone https://github.com/smangul1/rop.git

Install ROP from the base directory

cd rop
./install.sh

Download reference database

./getDB.py ~/

Run ROP analysis by a single command

./rop.py example/unmappedExample.fastq example/ropOut/

Find ROP analysis in example/ropOut/ directory. Learn more about ROP output here

ROP tutorial

Use the sidebar on the right to navigate ROP tutorial. Get started with a toy example of 2000 reads distributed with ROP package.

What is ROP

ROP is a computational protocol aimed to discover the source of all unmapped, which originate from complex RNA molecules, recombinant B and T cell receptors and microbial communities. We have tested ROP on 1 trillion reads from 10641 RNA-Seq samples across at least 54 tissues and 2630 individuals. The ROP accounts for 99.9% of all reads, compared to 82.9% by conventional mapping-based protocols. ROP is able to profile:

  • repeats
  • hyper-edited RNAs
  • circRNAs, gene fusions, trans-splicing events
  • recombined B and T cell receptor repertoires
  • microbial communities

The 'dumpster diving' profile of unmapped reads output by our method is not limited to RNA-Seq technology and may be applied to whole-exome and whole-genome sequencing.

Referencing ROP

Mangul, Serghei, et al. "ROP: Dumpster Diving in RNA-sequencing to find the source of 1 trillion reads across diverse adult human tissues." Genome biology 19.1 (2018): 36.

Presentations

Slides from my talk at ASHG are available here

Contact Us

Please do not hesitate to contact us (smangul@ucla.edu) if you have any comments, suggestions, or clarification requests regarding the tutorial or if you would like to contribute to this resource.

Licence

See the LICENCE.txt file

Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.
Press h to open a hovercard with more details.