There are two slight differences to the way that LiBiNorm counts reads compared to htseq-count:
- Reads that map to contigs where no genes are located in the reference annotation are counted as noMatch by LiBiNorm. Htseq-count ignores such reads
- LiBiNorm ignores transcripts of biotype "retained intron" in gtf files as, in practice, few reads map to the retained introns and their presence gives misleading results when estimating gene/transcript length.
- When a bam file contains multiple alternative mappings for a given read or read pair LiBiNorm only counts this as a single non-unique read or read pair. htseq-count counts the read multiple times.
"LiBiNorm count" can be run in a fully htseq-count compatible mode using the -z option.