Dear Lakshmanan,

If the purpose of your analysis is to count reads falling within each feature, you may consider using the featureCounts() function in Rsubread package. It takes only about 2 minutes to summarize 10 million reads into a count table. But it only accept SAM files (you can use samtools to convert your BAM files to SAM files) and it only works on unix. See ?featureCounts() for more info.

For your second question, if the pair of reads is indeed mapped as a pair, then the region between them will be covered as well if the two reads are on the same exon. But the reality is that not every read pair can be successfully mapped as pairs. You may get only one end mapped, or the two ends are mapped to two locations which have a distance much bigger than the average fragment lengths. In these cases, you don't even know what are the exons which lie between the two reads. 

Hope this helps.

Cheers,
Wei

On Jun 22, 2012, at 11:56 PM, Lakshmanan Iyer wrote:

> Hi
> My apologies for multiple posting if it happens-- I sent the last mails
> from other accounts which may not be registered with Bioc-list
> -Lax
> Two questions:
> 
> 1. Is readGapppedAlignmentPairs - the most efficient way to read a
> paired-end bam file with mulit-mapped reads?
> I am asking as it takes an enormous amount of time to process and load.
> 
> 2. How does one work with coverage on GappedAlignmentPairs  in the context
> of RNASeq?
> The simplest way is to consider each left and right read as separate -
> essentially loose the "paired" information and calculate coverage.
> However, if both the left and right pair reads fall within a feature of
> interest - say an exon, does it imply coverage of the region of the exon
> between the reads too
> 
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> 
>>>>>>>>>>>>>>>>>>>>>>>>>>> 
>  LLLLLLLLLL---------------------------RRRRRRRRRR
>                    ^^^^^^^^^^^^^^^^^
> 
> In the figure above, the exon is represented by ">" and L and R represents
> the left and right reads aligned to the exon.
> I am talking about the region represented by "^".  Do we assume coverage
> for this region too?
> Does Coverage on GappedAlignmentPairs do this?
> 
> -best
> -Lax
> Center for Neuroscience Research
> Tufts Univeristy School of Medicine
> Boston, MA
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


______________________________________________________________________
The information in this email is confidential and intend...{{dropped:8}}

