MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts

Table 1 Configurable parameters and default values for each read-to-feature assignation round

Round	Feature	Feature_output	Feature_biotype	Min_overlap	ml_flag
Small	Transcript	Transcript_name	Transcript_biotype	1	True
Long_exon	Exon	Gene_name	Gene_biotype	1	True
Long_intron	Gene	Gene_name	Gene_biotype	1	True

Note that long-RNA introns are by default defined by the full gene body coordinates

ISSN: 1471-2105