This directory contains PacBio HCGM (High-Confidence Genome Mappings, see below) GTF files generated within the GENCODE Capture Long-Seq project. 

Listed here are genome alignments of PacBio reads, with their strand information, as inferred from their intron motifs and polyA tail location (see Methods section of the paper for more details).

All files correspond to genome assemblies hg38 and mm10.

# File naming scheme:

<species>All_Cap1_<tissue>_<subset>.stranded.gtf.gz

where:
	species:
		"mm": mouse
		"hs": human

	tissue: self-explanatory

	subset:
		"HCGMs": Pacbio PacBio HCGM read alignments, i.e. with the following characteristics:
				- Uniquely mapped
				- Double-bounded: the read contains both library adapters (i.e., its cDNA insert is believed to be fully sequenced)
				- If spliced, its constituting introns must all be canonical (GT|GC/AG)
				- If unspliced, it must bear a detectable polyA tail