Hi,

BEDTools (http://code.google.com/p/bedtools/) can do that.

First of all you create a bed file (region.bed) of your chromosomal region; you can put more than one region into the file, for example:

chr1 10 50

chr1 500 1000

than you run the intersectBed tool from BEDTools suite, for example:

> intersectBed –abam reads.bam –b region.bed -bed

The output is the list of the read mapping that region, with additional information about the strand ecc...

If you just want to know the # of read mapping you can use in pipe the "wc" command:

> intersectBed –abam reads.unsorted.bam –b region.bed -bed | wc

Hope you find it useful.

Best regards

Thank's Alessandro Pietrelli. I understood your point. But I am looking at it in a different way. Is there any idenifier within the sam file that can quanify the number of reads aligned to a particular position or interval.

Try 'Tablet' - A Next Generation Sequence Assembly Visualization Software

http://bioinf.scri.ac.uk/tablet/