how to summarize information for a gene from bam file

[roll]

I have very basic question about bam files, it may be very obvious but kind of stacked.

I would like to see how many LINE,SINE etc are around the genes (which of my genes are enriched with repeats of LINE/SINE etc. elements).

For this, I have aligned data in bam format and the repeats in bed format.

As far as i know BAM files contains aligned data for each read from fastq file. How can i summarise information for each gene from a bam file? so that i can overlap these genes with the repeats and check for an enrichment?

[GenoMax]

You can use bedtools for this purpose. An example would be the multicov option: http://bedtools.readthedocs.org/en/l.../multicov.html

[shi]

I have very basic question about bam files, it may be very obvious but kind of stacked.

I would like to see how many LINE,SINE etc are around the genes (which of my genes are enriched with repeats of LINE/SINE etc. elements).

For this, I have aligned data in bam format and the repeats in bed format.

As far as i know BAM files contains aligned data for each read from fastq file. How can i summarise information for each gene from a bam file? so that i can overlap these genes with the repeats and check for an enrichment?

The featureCounts program may help - http://bioinf.wehi.edu.au/featureCounts/

[roll]

You can use bedtools for this purpose. An example would be the multicov option: http://bedtools.readthedocs.org/en/l.../multicov.html

Thanks, i was looking at this feature. It is fast but i also want to know the repeat elements that are within certain threshold, 500bp for example in the forward strand.
This seems to be possible with bedtools windows option (-l -r) but not sure if it works with multicov. At least there is no option in the help menu.