coverage of the reads over coding sequence only for one gene

Question

[alireza346]

I have RNAseq data and trying to get the coverage of the reads over coding sequence but only for one gene for example GAPDH. and plot the coverage in this way: in fact the y-axis would be coverage or normalized read count and x-axis would be the coding sequence. but the coding sequence which would be the x-axis will be shown between 0 to 100 (%). I have made the bam file for gapdh. do you know how to do that?

[guillaume.rbt]

You can use bedtools coverage to compute the coverage at every base of your gene, then use R to output a graph of coverage over the length of your gene. (I don't really get the "0 to 100%" part)

[Eric Lim]

I read it as the % is relative to everything, including non-coding regions of the gene.

[cpad0112]

try coveragebed -hist option from bedtools.