How to get the gene symbols for my bam file or bed file

Question

[vinaysbharadhwaj]

Hello, I am new to NGS and wanted to know which genes are present in my aligned file. I have performed BWA MEM to obtain a sam file and used picard to get a sorted.bam file. I also used bedtools to get a BED file and used its annotate utility to find the gene id or gene symbol for my reads. But it was only giving my the coverage. How do I get my gene symbols or gene ids using bedtools or any other tool?

Please Help

[WouterDeCoster]

Can you explain what your final goal is?

[vinaysbharadhwaj]

I want to get the genes that are present in my bacterial isolate and check with a database if that gene is virulent or rather the bacteria is virulent

[Devon Ryan]

Do you want the number of reads/pairs aligning to each gene or do you want to annotate each read with the gene it aligns to?

[vinaysbharadhwaj]

I want to annotate each read with the gene it aligns to

[Pierre Lindenbaum]

just curious: what would you with that information ?

[vinaysbharadhwaj]

I want to check if there are any virulent genes present in my bacterial sample

[Devon Ryan]

I strongly suspect that featureCounts would be easier then.

[vinaysbharadhwaj]

Thank you so much it worked very well

[Pierre Lindenbaum]

so as said Devon , what about just counting " the number of reads/pairs aligning to each gene" ?