how to calculate percentage of read distribution of each gene

[linjc]

Hi.
I'm a new guy in bioinformatics. I would like to calculate the percentage of read distribution of each gene from RNAseq data. For example, in A gene, 2% CDS reads, 10% 3‘UTR reads, etc. I need result of every gene in genome. Do any master know if there are some tools or scripts?
Thanks.

[GenoMax]

Use a bed file which has this annotation information. Then you would want to use bedtools coveragebed tool to get the information you need.

[shuelga@nugen]

You can download BED files for different genome regions using the UCSC Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables). Select your desired assembly (hg19?), group "Genes and Gene Predictions", track "RefSeq Genes", table "refGene", and output format "BED" then hit "get output". From there you can create BED files with filters for each of the regions you want, ie: exons, introns, 5'UTR, 3'UTR, coding, etc. Finally, BedTools intersect or coverageBed as @GenoMax has suggested can get you read counts in those regions that you can then group by gene.