How can I export numerical value?

[olmo...@gmail.com]

Hi, I am analyzing a Chip file comparing 2 cell lines. I am interested in a particular gene and I would like to generate a table with the numerical value for every single peak that compose the region. I am able to see those value if I go over the peak with the mouse but is there a way to export them all together in a table?
Thank you!

[James Robinson]

You can't do that with IGV,  but if you have a chip file you already have the data exported.  

On Thu, May 17, 2018 at 10:35 AM, <olmo...@gmail.com> wrote:

Hi, I am analyzing a Chip file comparing 2 cell lines. I am interested in a particular gene and I would like to generate a table with the numerical value for every single peak that compose the region. I am able to see those value if I go over the peak with the mouse but is there a way to export them all together in a table?
Thank you!

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/cb4b4591-9789-4c0d-aa4a-61081ffca11a%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[olmo...@gmail.com]

Thank you for your reply but I need the values for those peaks to be on a table, how do I identify this in the bed or tdz file? I mean I see the numbers on the peaks, there must be a way to get them in a table. It was a request from a journal for publication...
thanks

On Thursday, May 17, 2018 at 4:08:25 PM UTC-4, Jim Robinson wrote:

You can't do that with IGV,  but if you have a chip file you already have the data exported.  

On Thu, May 17, 2018 at 10:35 AM, <olmo...@gmail.com> wrote:

Hi, I am analyzing a Chip file comparing 2 cell lines. I am interested in a particular gene and I would like to generate a table with the numerical value for every single peak that compose the region. I am able to see those value if I go over the peak with the mouse but is there a way to export them all together in a table?
Thank you!

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

[James Robinson]

You would need to write a script to do it,  the details of the script would depend on the format of the file.    If you have or can create a ".bedgraph" file  you could use bedtools with a script to extract what you need.   In any event this is not something IGV does.

[olmo...@gmail.com]

Oh I see. Thank you very much for your help