I have paired-end sequencing data of RNAi target fragments from a genome wide RNAi library screen. Aligning the reads to the genome has proved relatively simple, but calculating the read depth with paired ends has been more difficult as my approach has not recognized the area between 2 ends on a single read as being covered. Instead only the region corresponding to the 70 bases read directly by the sequencing are considered covered on the genome.
Is there any way to calculate read depth in which the area between 2 ends of a fragment that is not directly sequenced are added to dead depth?
Alignment was done with Bowtie2 and the read depth calculated in artemis after processing with samtools.
I can provide more details if necessary.