Shotgun transcriptome sequencing covers gene sequences from the 5' to 3' ends. The transcript coverage for both the (a) random primer TSEQ and (b) Oligo DT sample preparation protocols are compared for short (< 2,500 bp), medium (>2,500 bp and < 10,000 bp), and long (> 10,000 bp) RefSeq genes. The x axis divides the transcripts into 20 bins from the 5' to 3' end and the vertical bars plot the number of unique reads that BLAST with e ≤ 10-20 into each bin for the long (blue), medium (red), and short (yellow) genes. The coverage is determined by counting the numbers of reads that align to the RefSeq sequence with 5' end in each bin. The apparent decrease of coverage at the 3' end for each method is due to reduced probability that the average 250 bp reads will start in the 3' extreme > 90% bins, for shorter genes < 2500 bp.
Mane et al. BMC Genomics 2009 10:264 doi:10.1186/1471-2164-10-264