Is their any identifier within the sam files which can give me the number of reads aligned to a particular chromosomal region.
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/
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