KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Deposited Data
GEUVADIS	Lappalainen et al. (2013)	SRA:ERR188297, ERR188088, ERR188329, ERR188288, ERR188021, ERR188356, ERR188145, ERR188347, ERR188382, ERR188436, ERR188052, ERR188402, ERR188343, ERR188295, ERR188479, ERR188204, ERR188317, ERR188453, ERR188258, ERR188114, ERR188334, ERR188353, ERR188276, ERR188153, ERR188345, ERR188192, ERR188155, ERR188132, ERR188408, ERR188265
Human Body Map	The Illumina Body Map 2.0 data	SRA:ERP000546
1000 Genome Trio short read	Clarke et al. (2016)	SRA:ERP012633
1000 Genome Trio long read	Chaisson et al. (2019)	SRA:ERP015321
Human Reference Genome GRCh38	Schneider et al. (2017)	ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/GRCh38.primary_assembly.genome.fa.gz
Gencode annotation v26	Frankish et al. (2018)	ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_26/gencode.v26.annotation.gtf.gz
Software and Algorithms
SAD	this work	https://github.com/Kingsford-Group/sad
Salmon	Patro et al. (2017)	https://salmon.readthedocs.io/en/latest/
RSEM	Li and Dewey (2011)	https://deweylab.github.io/RSEM/
STAR	Dobin et al. (2013)	https://github.com/alexdobin/STAR
Scallop	Shao and Kingsford (2017)	https://github.com/Kingsford-Group/scallop
StringTie	Pertea et al. (2015)	http://ccb.jhu.edu/software/stringtie/
gffcompare	Pertea (2018)	http://ccb.jhu.edu/software/stringtie/gffcompare.shtml
Polyester	Frazee et al. (2015)	https://github.com/alyssafrazee/polyester
samtools	Li et al. (2009b)	http://samtools.sourceforge.net/
eXpress	Roberts and Pachter (2013)	https://pachterlab.github.io/eXpress/index.html