However, the transcript lengths in these expression sites differ.
The transcript lengths had a median of 380 bp and a mean of 992 bp (standard deviation = 1363 bp), and ranged between 201 bp and 24,848 bp (Additional file 1 shows the length distribution of assembled transcripts).
The selected expression measurement was the Reads per Kilobase of exon model per Million mapped reads (RPKM) with the aim of normalizing for the difference in number of mapped reads between samples, as well as the transcript length [ 35].
The best alignments between transcript and genome annotation (those spanning at least 90%% of the transcript length) were selected and subsequently clustered in groups based on a minimum overlap of 30%% between alignments.
Generally, FC shows the relative difference between two samples and ARPK is the expression level of a transcript normalized by the transcript length.
A 3-fold difference in the median number of duplicate reads between AS and SMS across all transcripts observed in all samples was maintained across the majority of the transcript length (Figure 2D).
18 24 % gene transcripts were covered across their full length (90 100%% of the transcript length) and 17 18 % of genes were covered for less than 10%% of their transcript length.
As could have been expected there was a negative correlation between the mouse transcript length and the fraction of transcript covered by the bank vole sequences, although this effect was rather weak (R2 = 0.077, P < 10-4; transcript length log-transformed, fraction covered arcsin-sqrt transformed) (Fig. 6).
A fixed length of 225 nucleotides was calculated to provide the best fit between the peak locations and the known transcript lengths.
Below, we propose a molecular explanation for this finding, based on the known relationship between transcript length and the stability of eIF4F-cap interaction [ 20].
