Release Title: v1.0.0 - September 9, 2024
Overview
We are thrilled to introduce the first release of the multiClassPromoterCuration v1.0.0 ! This initial release includes R-scripts for curating the promoters of following gene class:
i) Non Coding RNA types from RNAcentral
ii) Protein Coding Genes from GENCODE
iii) Repeats from RepeatMasker
Features
i) Clustered the TSS of similar RNA types that are within 120 nucleotides (Genes in positive and negative strand of DNA are clustered separately. Repeats from RepeatMasker were not clustered)
ii) Median of the TSS is found for each cluster. Promoter window spans from 50nt upstream to 200nt downstream of the median TSS.
iii) All the gene informations of clustered TSSs are collapsed in a single row.
Usage
Run the 6 steps R Script files to generate the final file "MultiClassPromoter.tsv" that contains information of promoter and gene of all RNA types.
Additional Information
The input files are trimmed down for the fast processing of the code and the easy upload in GitHub. Kindly update the following files with their full version by downloading from their respective servers:
i) REPEATMASKER.tsv (update from repeatmasker website )
ii) homo_sapiens.GRCh38.bed (update from RNAcentral website)
iii) files in the folder ./database/ (update from RNAcentral associated databases from RNAcentral website)
iv) ENSEMBL.tsv (update from GENCODE website)
Support
For questions or support, please contact us at kvbortle@illinois.edu or open an issue on GitHub Issues.