Loading bam files and its index to the alignment track

[Rehema Shungu]

I have tried to load the bam files to the alignment track, the weird thing for the past few days it worked perfectly but today since morning. it shows every data loaded from the server but not the .bam and .bai files

what caused this? and how can I resolve it?

[igv-help]

Unless you've just updated to a different version of IGV, clearly nothing changed on the IGV end to cause this. But if you provide more details we might be able to see why IGV cannot load your files.

The following information might help:

- IGV version 

- The IGV log (see the file" igv0.log" in the "igv" folder under your home folder)

- How you loaded the files, and where they are located

- What do you mean it does not show the files? Does IGV not even create a track? Or does it create a track, but the data is not loaded? If so, are you viewing a locus where you know there is data?

- Seeing screenshot images will often help, and screencast videos can be even better.

Helga

[Rehema Shungu]

1. For the IGV log file, I have two - igv0log and igv1log file, please the above photo

2. The IGV version is 2.11.9, downloaded the MacOS app with Java included from the site https://software.broadinstitute.org/software/igv/download

3. the files were in my downloaded folder, hence File --> Load from file --> Downloads  -->Select the bam file ( next to it index, .bai)

I even tried to select & load both .bam and .bai, no success

4. as you can see below, the bam file is loaded but no alignments or coverage tracks can be seen. Yes, I did try to search for a specific chromosome position chr9-129,130,168-129,130,212 to the last zoom in level.  but still no luck. but two days ago, it worked perfectly.

Thanks in advance

[igv-help]

In the screenshot you sent of the log, there's an error because a bam file has been loaded via the Genomes menu. It needs to be loaded from the File menu.

Helga
 

[Rehema Shungu]

I only loaded from the genome as part of troubleshooting the problem. but it didn't work also. so

[igv-help]

If you send the log that corresponds to a run of IGV where you are seeing the problem we are trying to track down, it's possible it might have clues as to what is going on.

One thing to try might be to move your files to a different folder. The "Downloads" folder is one of the special folders with tighter access restrictions on recent versions of MacOS. Try putting the bam & bai in a folder that is not under any of the following: Downloads, Desktop, Documents, network drive.

Helga