gap-free alignment

[nufangdeshengming]

"RSEM comes bundled with the Trinity software distribution. The RSEM protocol currently requires gap-free alignments of RNA-Seq reads to Trinity-reconstructed transcripts, such as alignments generated by the Bowtie software."
In order to compare expression levels of different transcripts or genes across samples, a Trinity-included script invokes edgeR to perform an additional
TMM (Trimmed Mean of M-values) scaling normalization that aims to account for differences in total cellular RNA production across all samples."
I see this in the trinity protocol,and i donnot konw what are the "gap-free alignments" ,and i hope someone would help me explain this.Also,what is TMM (Trimmed Mean of M-values) ?
many thanks.

[gringer]

A gap-free alignment has no INDELs. Here's an alignment with a gap:

GATTACA
GA-TACA

And here's an alignment without a gap:

GATTACA
GAGTACA