coverage RNAseq

[Trudy]

I would like to determine the coverage of mapped reads in exons, introns and intergenic regions.
Are there tools that could help me?

Thanks

[mbblack]

Do you have access to any commercial programs? ParTek will generate such a summary report, after indexing to Refseq, Ensembl or AceView transcripts (or a custom annotation that you create).

You should also be able to do this with bedtools and you could use UCSC Genome Table Browser to get the appropriate regions as BED files. If you select, for example, "knownGene" and give your output a file name, then click "get output" you will go to a screen where you can select exons, introns, and so forth.

bedtools includes a "coverageBed" tool (compare one BED file of reads to another you've created from the UCSC Table Browser) and "complementBed" could be used to get the intergenic regions.

I've not used bedtools for this though, since I have a Partek license, I went with that.