Table 2.

RNAdetector’s supported analysis, species, RNA types and files

Feature	Description
Input Files	FASTQ; BAM; SAM
Supported Analysis	Quantification; Differential expression analysis; Pathway analysis
Supported Species	Human; Mouse; C. elegans. Additional sequenced species can be analyzed by uploading their genome and\or transcriptome in FASTA format following the step-by-step procedure detailed in the user interface
Supported RNA types	mRNAs; miRNAs; snRNAs; snoRNAs; piRNA [only for human at this moment]; tsRNAs; tUCR [only for human at this moment]; lncRNAs; circRNAs. Additional ncRNAs classes can be analyzed by uploading their genomic coordinates in GTF or BED format following the step-by-step procedure detailed in the user interface
Output Files	Graphical final report for both Differential Expression Analysis and Pathway Analysis with summary of the results, figures, and tables. Text files with raw counts, normalized counts, differentially expressed gene and perturbated pathway can also be downloaded