Reference genomes and transcripts

Genome Reference

Human

GRCh38 (UCSC hg38) and corresponding index, ENCODE version reference with SIRVs added

Mouse

GRCm38 (UCSC mm10), using UCSC/ENCODE/UCSC

Manatee

https://www.ncbi.nlm.nih.gov/assembly/GCF_000243295.1/

Transcriptome Reference

Human

GENCODE v29 Including modified SIRVs.

Mouse

GENCODE M21 Including modfied SIRVs.