Question: coverage of the reads over coding sequence only for one gene
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gravatar for alireza346
2.7 years ago by
alireza3460
alireza3460 wrote:

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?

rna-seq • 612 views
ADD COMMENTlink written 2.7 years ago by alireza3460

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)

ADD REPLYlink written 2.7 years ago by guillaume.rbt830

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

ADD REPLYlink written 2.7 years ago by Eric Lim1.7k

try coveragebed -hist option from bedtools.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by cpad011215k
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