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samtools depthbut may I ask why you want to do that?I have to plot that expression. I have RPKM values for that gene but if I plot in the excel file it comes like a point. my idea is like showing the distribution of the expression. lets say x-axis is a length of the gene in the y-axis expression of the gene.
I do not really see how this would make sense. Gene coverage in RNA-seq is the sum of transcript/exon coverage so you cannot easily get a representative per-base coverage. Yes, gene expression is commonly reported as one value per gene, be it the RPKM metric or any other normalized expression value. What do you think would you gain from plotting a per-base coverage of a gene? Are you referring to exon usage?
actually it is not a gene. it is a snoRNA. Just for saying i wrote as a gene. but when i try samtool depth
i got error
"Does the file "PC1_Yale_PRS_sorted.bam" really contain a list of files and do all exist?"
I really don't know???