How to add read depth to gene of my interest

Question

[Govardhan Anande]

Hello,

I got few samples of RNA seq, I have done differential expression analysis.

Lets say my gene of interest is "X", Now I want to represent reads covering X gene in all samples, In other word I want to graphically represents read dept for X.

For example :

Thanks

[Govardhan Anande]

Hi Guys,

Thanks for the answer, however I have aligned reads to hg19 using bowtie2, then I filtered out reads aligned to X gene based on genomic coordinates.

Now I am about to generate figure by using IGV, but still its not that much impressive.

As Andrew mentioned I might try ggbio or ggplot2.

Thanks

[Michael]

Your example gene model looks incomplete, it looks like you are missing at least 2-3 exons. If this is is your gene of interest, you should at first validate the transcript, best experimentally.

[Govardhan Anande]

My gene of interest is tet1 bro, i just gave x for example.

Answer 1

[chen]

1, do alignement using bwa or other software
2, do per-loci statistics using samtools flagstat
3, plot the data with any tool your like

[WouterDeCoster]

I guess step 3 is his problem and 'any tool you like' is not a helpful suggestion.

[andrew.j.skelton73]

Actually, I think he does a pretty good job at answering the question, no need to put the user down if you haven't got anything constructive to offer yourself. A combination of ggbio and ggplot2 would be able to plot the gene track, along with a histogram.

[WouterDeCoster]

Considering that OP already performed differential expression analysis I consider step 1 and 2 as listed above her already performed.

[andrew.j.skelton73]

I consider step 1 and 2 as listed above her already performed

With tools like Kallisto and Salmon, alignment isn't strictly necessary for RNA Seq differential expression analysis anymore, but either way, my point is just to have a bit of courtesy, rather than deconstructing other people's answers.

[WouterDeCoster]

Deconstruction was certainly not what I had in mind and if my post, which in hindsight can be misinterpreted, was understood as such, I would like to apologize.