sequence bias correction in base coverage calculation

[lher]

Hi,

I have 76 bp Illumina HiSeq yeast mRNA seq data and would like to do a combined analysis of sequence coverage over a set of ~500 transcripts, which are all aligned in a range from 1 to 1000.
However, the combined coverage profile is still noisy and shows many artificial peaks.
Is there a way to account for sequencing biases and then modify the genome coverage file (e.g. bedgraph) respectively?

Thanks for any suggestions!