Please check out the publication if you interesting in this tool and the github.
The COMRADES experimental protocol for the prediction of RNA structure
in vivo was first published in 2018 (Ziv et al., 2019) where they
predicted the structure of the Zika virus. The protocol has subsequently
been use to predict the structure of SARS-CoV-2 (Ziv et al., 2020). Have
a look to get an understanding of the protocol:
COMRADES determines in vivo RNA structures and interactions. (2018). Omer Ziv, Marta Gabryelska, Aaron Lun, Luca Gebert. Jessica Sheu-Gruttadauria and Luke Meredith, Zhong-Yu Liu, Chun Kit Kwok, Cheng-Feng Qin, Ian MacRae, Ian Goodfellow , John Marioni, Grzegorz Kudla, Eric Miska. Nature Methods. Volume 15. https://doi.org/10.1038/s41592-018-0121-0
The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2. (2020). Omer Ziv, Jonathan Price, Lyudmila Shalamova, Tsveta Kamenova, Ian Goodfellow, Friedemann Weber, Eric A. Miska. Molecular Cell, Volume 80 https://doi.org/10.1016/j.molcel.2020.11.004
After sequencing, short reads are produced similar to a spliced / chimeric RNA read but where one half of the read corresponds to one half of a structural RNA duplex and the other half of the reads corresponds to the other half of the structural RNA duplex. This package has been designed to analyse this data. The short reads need to be prepared in a specific way to be inputted into this package.
There are other types of crosslinking data!
Fastq files produced from the COMRADES experiment can be processed for
input into rnaCrosslinkOO using the Nextflow pre-processing pipeline, to
get more information visit here. The
pipeline takes the reads through trimming alignment, QC and the
production of the files necessary for input to rnaCrosslinkOO.
Crosslinking experiments often have different library preparation
protocols therefore it is not necessary to follow the prescribed
pre-processing pipeline. The only requirement is that the input files
for rnaCrosslinkOO have the correct format detailed below.
The main output files are the files entitled X_gapped.txt.
These are the input files for rnaCrosslinkOO. The columns of the output
files are as follows: