There are several methods to normalise the raw reads counts, such as RPKM (FPKM for pair-end), TPM, TMM, and so on. To remove the effect of gene length, they will divide the raw counts by the gene length, since long genes tend to have more counts mapped to them. But I read from some paper that you should use "effective length" instead of gene length (Pachter, Lior. "Models for transcript quantification from RNA-Seq." arXiv preprint arXiv:1104.3889 (2011)). And the "effective length" equals: gene length - sequencing depth(or reads length) + 1, which is also the number of positions in which a read can start.
But what if the gene length is shorter than the sequencing depth? Because then you'll get a negative effective length. And if you use the negative value to divide the raw reads counts, then you'll also get a negative normalised value in the matrix of RPKM or TPM.