KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited data
RiboMinus RNA-seq data	Ji et al., 2019	https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA000751
RNA-seq data	Ji et al., 2019	https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA000751
RNase R+ data	Ji et al., 2019	https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA000751
Polymorphism data	IGSR	ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/GRCh38_positions/
Genome assembly and annotation data	ENSEMBL	http://may2017.archive.ensembl.org/index.html
Software and algorithms
R	The R Foundation	https://www.r-project.org/
Perl	The Perl Foundation	https://www.perl.org/
Python	Python Software Foundation	https://www.python.org/
LiftOver	UCSC	https://genome.ucsc.edu/util.html
BioMart	ENSEMBL	http://useast.ensembl.org/biomart/martview//38de6b77bceb11d76acd2a1d1b231382
BWA	Li and Durbin 2009	http://bio-bwa.sourceforge.net/
Tophat2	Kim et al., 2013	https://ccb.jhu.edu/software/tophat/index.shtml
STAR	Dobin et al., 2013	https://github.com/alexdobin/STAR
CircExplorer2	Zhang et al., 2016	https://circexplorer2.readthedocs.io/en/latest/
CIRI2	Gao et al., 2018	http://159.226.67.237:8080/new/download_file.php