Experiment: deep sequencing for mutants in 700nt fragment.
the fragment of dna was preamplified by primers flanking the fragment followed by hiseq.
per base coverage was calculated by coverageBed -d -abam in.bam -b ref.bed > out.cov
Observation: two distinct peaks in coverage at the ends as below plot.. coverage vs positions
the peaks are made from reads having part of primers..thus also show soft clipping at ends..
there is a huge difference in the calculations if i include such reads And if I exclude them.
Question: is there anyone who knows how to handle such a situation?