This repository contains the code for the LIBD collaboration with Luigi Marchionni's group at Johns Hopkins University (JHU) and RIKEN with data from FANTOM and recount2. The results from this project are already been used by FANTOM6.
In detail, this repository contains the code for running recount.bwtool on a set of FANTOM6-derived annotations. In particular, the work by Imada, Sanchez, et al, bioRxiv, 2019 DOI 10.1101/659490 focused on disjoint elements across each strand that you can find at djnUnstrand. For each of strand (and the combined version) we ran recount.bwtool using scripts such as djnPos_rse.sh. The output was then processed by scripts located in the eddieimada/fcr2 repository.
If you use this data, please cite Imada, Sanchez, et al, bioRxiv, 2019, DOI 10.1101/659490. Here's a BibTex entry you can use:
@article {Imada659490,
author = {Imada, Eddie-Luidy and Sanchez, Diego Fernando and Collado-Torres, Leonardo and Wilks, Christopher and Matam, Tejasvi and Dinalankara, Wikum and Stupnikov, Aleksey and Lobo-Pereira, Francisco and Yip, Chi-Wai and Yasuzawa, Kayoko and Kondo, Naoto and Itoh, Masayoshi and Suzuki, Harukazu and Kasukawa, Takeya and Hon, Chung-Chau and de Hoon, Michiel JL and Shin, Jay W and Carninci, Piero and , and Jaffe, Andrew E and Leek, Jeffrey T and Favorov, Alexander and Franco, Gloria R and Langmead, Ben and Marchionni, Luigi},
title = {Recounting the FANTOM Cage Associated Transcriptome},
elocation-id = {659490},
year = {2019},
doi = {10.1101/659490},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2019/07/08/659490},
eprint = {https://www.biorxiv.org/content/early/2019/07/08/659490.full.pdf},
journal = {bioRxiv}
}
JHPCE location: /dcl01/ajaffe/data/lab/marchionni_projects