[Bioc-sig-seq] NA vector for alignQuality with Bowtie output

[Steve Lianoglou]

Hi,

On Dec 1, 2009, at 8:02 AM, Ramzi TEMANNI wrote:

> Hi Martin,
> 
> Thanks for the info, I was mixing between reads quality and alignment
> quality
> Indeed there' no info about alignment Quality on bowtie output and reads
> quality could be extracted using quality() accessors.
> 
> I'm trying to generate mate pair data from single read data by aligning
> single reads (1/2) then look at the id and recover aligned pairs based on
> their
> ID. I'm trying to find out structural variations mainly fusion genes where
> mate 1 & 2 belong to different chromosomes. I'm trying to filter the data by
> keeping only pairs belonguing to diffrent chromosomes, but the final number
> is high around 20000 reads and it's very high so i'm looking for further
> filtering to remove artefact from there.

This isn't really here nor there, but just out of curiosity: is the number of reads (20,000) really that high? How many reads are in your sample?

Or are the number of different loci that these reads map to higher than you expected? Or, to put it another way, why are you expecting the number of such events to be so low? :-)

-steve

--
Steve Lianoglou
Graduate Student: Computational Systems Biology
  |  Memorial Sloan-Kettering Cancer Center
  |  Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact