Question: How to add read depth to gene of my interest
0
gravatar for Govardhan Anande
3.6 years ago by
Australia
Govardhan Anande130 wrote:

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 :

enter image description here

Thanks

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Govardhan Anande130

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

ADD REPLYlink written 3.6 years ago by Govardhan Anande130

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.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Michael Dondrup46k

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

ADD REPLYlink written 3.6 years ago by Govardhan Anande130
4
gravatar for chen
3.6 years ago by
chen1.9k
OpenGene
chen1.9k wrote:

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

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by chen1.9k
1

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

ADD REPLYlink written 3.6 years ago by WouterDeCoster42k

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.

ADD REPLYlink written 3.6 years ago by andrew.j.skelton735.8k

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

ADD REPLYlink written 3.6 years ago by WouterDeCoster42k

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.

ADD REPLYlink written 3.6 years ago by andrew.j.skelton735.8k
2

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.

ADD REPLYlink written 3.6 years ago by WouterDeCoster42k
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