[Bioc-sig-seq] Paired end reads -tools?

Paul Leo p.leo at uq.edu.au
Mon Oct 26 02:31:13 CET 2009


I have some low coverage paired end data. I would like to plot the
difference between the paired end reads. 

I've used Shortread, IRANGES etc some but have not seen explicit use of
paired end data ... I'm not quite sure how that data is handled in
IRANGES as a RangedData object?

Would be grateful any pointers or ideas on what others have used to
analyse this data.... looking for structural varions in matched
cancer/normal based on  paired in read  distance( data is very low
coverage so I think this is all I can hope for at the moment...)

Thanks
Paul



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