CRAM to IGV

[Divine Marcelino]

Good day.

I am trying to open some files through IGV, however, I am unable to open some of the cram files I have and whenever I try to load them through IGV, it just states that it is not found. I tried using both the web interface and the offline IGV app to see if it makes any difference but both state the same thing.

I am unsure what next steps I could take so I could open these files.

Thank you!

[igv-help]

How are you trying to load them exactly?  There's not enough information here to help you.

[Mela]

Hello,

With the use of my IGV application from my MAC, i load the data using "load genome frorm URL" which I could find from terra. 

Thank you

Mela

--

---
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.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/428e3578-ac2b-46fb-8514-eae308646cedn%40googlegroups.com.

[igv-help]

Well, as you note, the server is telling IGV that the file is not found.   This can be for 2 reasons,  (1) it really isn't there, or (2) you aren't authorized to view it.     

What happens if you paste the URL you are loading into IGV in a web browser window?

[igv-help]

By that I mean just try to load it directly from the web browser.   This won't do anything useful, but does it start to download the file or does the web browser also display "file not found"

If it starts to download the file you can just cancel the download.

[James Robinson]

Also I suggest you contact the "Terra" team as this is not an issue on the client (IGV) side.   It is simply displaying the error message ("Not Found") the server is returning.

[Mela]

Hi James,

I tried loading the data directly from the web browser. Some data samples have successfully loaded but there are other samples that do not. They would only keep showing error loading track data. 

In this example, I have loaded 5 samples under 1 family. 3 samples loaded, 2 did not. 

Thank you

Mela

On Fri, Oct 27, 2023 at 12:08 PM James Robinson <jrob...@broadinstitute.org> wrote:

Also I suggest you contact the "Terra" team as this is not an issue on the client (IGV) side.   It is simply displaying the error message ("Not Found") the server is returning.

--

---
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.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CACOP%2BpsQw4nN1zYJaSO_J2_z-WqZL45EER9aem0GtyF6DAmg8g%40mail.gmail.com.

[James Robinson]

Hi,  I wasn't suggesting you try to load data into IGV from the web browser, but rather that you paste the url that is giving the "not found" error into the address bar of your web browser and hit return.   Nothing to do with IGV, just the web browser,  to see what happens.

There is really nothing IGV can do if the server returns "Not Found" for a url.   You will need to contact Terra support about that. 

You received this message because you are subscribed to a topic in the Google Groups "igv-help" group.
To unsubscribe from this topic, visit https://groups.google.com/d/topic/igv-help/__n-4zqvQCQ/unsubscribe.
To unsubscribe from this group and all its topics, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/CAOHmXyyoV57bK_4ta47UbVcEFyX%2BVA0vawaWbesHT7SGviY4mA%40mail.gmail.com.