read pairs to fragment coordinates

[touchsk]

Hi All,

I have a bam file from the alignment of paired-end NGS data to the human genome. Most of these read-pairs are non-overlapping. Is there any tool that takes this bam as input and provides the merged coordinates from the pairs.

Eg:
Read1-FWD: chr1 1 20
Read1-REV: chr1 80 100

Result: chr1 1 100

If only one read is aligned, then ignore its mate. If the alignment is on opposite strand, reverse for that.

I know a lot of tools estimate fragment size, but do they output results like above as well? I can write a quick script for this, but was wondering if something was already available.
Many thanks.

[ashishbansal]

We introduce a profile homology search tool named Short-Pair that is designed for short paired-end reads. By using an approximate Bayesian approach employing distribution of fragment lengths and alignment scores, Short-Pair can retrieve the missing end and determine true domains. In particular, Short-Pair increases the accuracy in aligning short reads that are part of remote homologs. We applied Short-Pair to a RNA-Seq dataset and a metagenomic dataset and quantified its sensitivity and accuracy on homology search. The experimental results show that Short-Pair can achieve better overall performance than the state-of-the-art methodology of profile homology search.