Retrieving specific gene location

Question

[akylzhanov.r]

Dear All The application being used is Integrated Genome Viewer (IGV).

I have a bedgraph file with the values to analyze.

The aim is to look up the values of the specific genes (names are given) in the bedgraph file.

I go and specify Regions->Gene Lists and can see heat map of the genes specified. In the fill tab between Chromosome Number and Go button I can see the coordinates of a gene in the chromosome

gene= (chrA chromA_start ChromA_end DataValue_A).

How can I export the coordinates of the genes from my list in Regions->Gene Lists to some csv/text file??

Thanks,a lot.

[reza.jabal]

File > Save Session will do the work. It will produce an .xml output!

[akylzhanov.r]

Thank you. That really works. The left thing to do is pickup the selected genes knowing their location in chromosomes. It would be awesome if you knew the standard built-in ways to do that!

[reza.jabal]

There are numerous approach toward this, but I guess the most straightforward one is to paste your chromosome boundaries [column D in your .xml file] into UCSC genome browser. for this:

https://genome.ucsc.edu/ > from the tools drop-down list > Table Browser > define regions

and then customize your output as you desire. Hope it helps!

Answer 1

[jotan]

IGV is not the right tool for the job.

You want to intersect your list of genes against your bed graph file. If you have no other available to you, use galaxy.

Upload your bedgraph file. Upload the coordinates of the genes you're interested in.

On the left hand panel, under "operate on genomic intervals", select Join.

Read instructions and run.