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Old 10-03-2013, 03:30 AM   #1
tospo
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Default Viewing multiple BAM files in Artemis

Not a question - just found out how to do this and I don't think this is particularly well documented, so just posting this here to help other users.

To compare several BAM files in Artemis, first load one BAM file (File > Read BAM / VCF), then right-click in the BAM window and choose "Add BAM". The reads from the two BAM files will be merged into the one window, so the trick is to right-click again and select "Clone Window".

Now you have two BAM windows with the same merged reads view. Right-click into each one individually and choose "BAM files", which brings up a tick-box list of the loaded files. Now select a different active BAM file in each window to end up with two windows, each showing only the reads from a single BAM file.
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Old 12-11-2013, 12:09 AM   #2
Soni
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Thanks for posting this tospo.

I tried it but it's still not working. The second .bam file I load doesn't appear in the cloned window. Only the first one does. I tried several views too but with no luck. When I reverse the order of bam files the same happens. The first one appears but the second one doesn't. I'm using version 15.0.0 of Artemis.

Any idea what might be going on?

Cheers
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Old 12-11-2013, 12:23 AM   #3
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Hi Soni,

You say that the second bam file doesn't appear in the cloned window. Does it appear in the original window then, i.e. does the window before cloning have two bam files and can you select both of them when you right-click into the window and select "BAM files" from the context menu?
Can you post a screen shot?
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Old 12-11-2013, 05:15 AM   #4
Soni
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Hi topso.
Yes I can load both the files (see screenshot 1 below).
When I clone the window and select a different bam file to appear in each window I get screenshot 2.

Cheers
Attached Images
File Type: png Both bam files loaded.png (127.6 KB, 4 views)
File Type: png cloned window 2nd bam selected to view in top window.png (125.0 KB, 2 views)
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Old 12-11-2013, 05:21 AM   #5
tospo
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hard to see on the screenshot but are you sure the top window isn't simply scrolled all the way up so you don't see any reads? I'm sure you've tried this already but just in case... can you try to drag the scroll bar handle at the right-hand side of the top window all the way down?
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Old 12-11-2013, 05:25 AM   #6
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In addition: are you starting artemis on the command line? If you do (and I recommend doing it) you have a lot of options that you can set in the command line, which is very handy for quickly firing off artemis on different files.
This command will start artemis with two separate bam windows, each showing one file:

Code:
art -Dbam1 first_file.bam -Dbam2 second_file.bam
There are lots of other options as well (have a look at the manual). It really is the best way to run artemis.
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Old 12-17-2013, 11:04 PM   #7
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Thanks tospo. It worked through the commandline.
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