number of reads per region of interest

[Schelarina]

Hello,
I want to calculate the number of reads mapped to my reference in each gene, in the intergenic regions, in introns, in rRNA and tRNA.
I have bam and gff files. Which commands can I use?
Thanks for your help

[GenoMax]

BEDTools multicov: http://bedtools.readthedocs.org/en/l.../multicov.html

If you need a visual program: http://seqanswers.com/forums/showthread.php?t=47028

Samtools depth option: http://seqanswers.com/forums/showthread.php?t=45399

[Michael.Ante]

You can use RSeQC's read_distribution.py function (with a given bed file) to get a first glance at your data.
With HTSeq-count you get the gene read count. (Be aware of the strand information of your data). Additionally, if your gtf has information of the genes' bio-type (protein_coding, rRNA, etc.), you can count the reads for each of these classes.