TABLE 1.

Recent tools for transcription and small RNA analysis.

Tool	Function	Input data	Algorithm for read mapping and selection	References
SalmonTE	Quantification of TE transcript abundance	RNA-seq and TE sequences	EM-algorithm	Jeong et al. (2018)
Telescope	Copy-specific TE expression	Aligned read from RNAseq	EM-algorithm	Bendall et al. (2019)
TEtools	Determine differentially expressed TEs and smallRNAs	SmallRNA-seq, RNA-seq, TE copies	Bowtie2 (mRNA) and Bowtie1 (smallRNA) (random assignment of best match)	Lerat et al. (2017)
REdiscoverTE	Copy-specific TE expression	RNA-seq, TE copy sequences, intron sequences	Salmon (EM-algorithm)	Kong et al. (2019)
ExplorATE	Copy-specific TE expression	Genome sequence, gene annotation, TE annotation RNA-seq	Salmon; target transcript assignation based on the percentage of identity for a class/family of TEs	https://github.com/FemeniasM/ExplorATE_shell_script
TEffectR	Influence of TEs on neighboring gene expression	Gene annotation, TE annotation, aligned RNA-seq reads on genome	Reads with 100% overlap with given TE regions are considered	Karakülah et al. (2019)
LIONS	Identification and analysis of chimeric TE-gene transcripts	RNA-seq, References genome, gene and TE annotation	Tophat2 (random assignment of best match)	Babaian et al. (2019)
PiPipes	Analyze piRNAs and TE-derived RNAs	SmallRNA-seq, RNA-seq, TE copies	STAR (mRNA) and Bowtie1 (smallRNA) (EM-algorithm)	Han et al. (2015)
PingPongPro	Detection of ping-pong cycle activity in piRNA-Seq data	SmallRNA-seq	Weighted read count	Uhrig and Klein, (2019)