Hi Paul,
First to clarify, are you talking about paired-end (insert size of
around 200bp) or mate-pair (insert size of around 2-3kb) sequencing?
I've been doing some analysis of mate pair data in R (for a de-novo
assembly). The synopsis of what I've done is (I can elaborate if you
think what I've done is of interest for you):
1) load the aligned reads
2) filter them for N containing reads, reads aligned to non-ref
chromosome, etc
3) identify the uniquely mapped mate pair, i.e. each mate map only
once in the genome and has a single mate (computationally performed
using their ids)
4) convert the mate reads into intervals stored into a RangedData object
5) estimate the insert size distribution and further processing
(assembly in my case)
In your case, if you're using mate pairs (I hardly see how to do that
with "standard" paired reads), you could have a window sliding along
your chromosome and estimating whether the insert size in your cancer
sample is different from the one in the normal sample.
Best,
Nico
---------------------------------------------------------------
Nicolas Delhomme
High Throughput Functional Genomics Center
European Molecular Biology Laboratory
Tel: +49 6221 387 8426
Email: [email protected]
Meyerhofstrasse 1 - Postfach 10.2209
69102 Heidelberg, Germany
---------------------------------------------------------------
On 26 Oct 2009, at 02:31, Paul Leo wrote:
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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