Visualizing with samtools?

[Adamo]

Hi,

I have some difficulties in manipulating BWA and samtools.
I have sorted my alignment stored in the .bam file, and indexed it (so I have a .bma and a .bam.bai).
To visualize the sequences, I've tried to use commands like view or pileup, but I find it very difficult to manipulate.

Is there a way to view the alignment (I've tried IGV, but I haven't been able to see the reads, only the reference genome) user-friendlier?
Or maybe I used the wrong input when using samtools...

Thanks in advance, I'm very new to bioinformatic...

[imilne]

Give Tablet a go - http://bioinf.scri.ac.uk/tablet

We've tried to make it as easy to use as possible (although there's always room for improvement, so if something doesn't make sense, just let us know).

Iain

[Adamo]

I'll give it a try, thanks.

[Adamo]

I have a few questions...
It seems like the soft only take into account the reads that map with the part of genome in the area of the viewing bar. Can I change it so that all the reads that map with chr2, for example, could be counted even if the whole chr2 isn't displayed?
Plus, reads are not always shown in the overview due to the scale... they are, as a consequence, difficult to locate. Is there some command to reach a read directly, avoiding me to manually search it? Or at least, maybe I can zoom in the overview so that i can locate a read more easily, have a look at it and then zoom out in the overview while keeping having the read aligned on the screen...?

I've read the user guide, but couldn't find those informations.

[imilne]

I have a few questions...
It seems like the soft only take into account the reads that map with the part of genome in the area of the viewing bar. Can I change it so that all the reads that map with chr2, for example, could be counted even if the whole chr2 isn't displayed?

That's because of the way BAM files work - they're designed so you can just peek at small parts of a massive data set without having to load everything into memory, but that means you don't know how many reads are associated with a contig unless you read all of it. Tablet doesn't do that unless you tell it to (by adjusting the BAM window width), and even then it can only give you details on the current contig and not the others.

If your data isn't that large (ie < 1GB), convert it back to sam and Tablet will process the entire file in one go. It'll take longer to load, but it'll give you the information you're after.

Plus, reads are not always shown in the overview due to the scale... they are, as a consequence, difficult to locate.

It's an overview - nothing more. Ultimately you can't fit 1,000,000 pixels into 500, so something has to be lost. If you want to zoom the overview for more detail for a given region, then just CTRL+drag on it to highlight the section to zoom. You might also find using the Coverage overview more useful.

Is there some command to reach a read directly, avoiding me to manually search it? Or at least, maybe I can zoom in the overview so that i can locate a read more easily, have a look at it and then zoom out in the overview while keeping having the read aligned on the screen...?

You can either search for a read by name, or use the "Jump To" option to move the display to a given location.

Iain

[seq_GA]

I tried the linux version and completed the installation.
How to open the tool. The following directories are available after the installation.

uninstall
tablet
jre
docs
lib
utils
tablet.vmoptions
output.log

I tried opening as in the command line./tablet But nothing happenes and i get the output log as below:

java.lang.ExceptionInInitializerError
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source)
        at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source)
        at java.lang.reflect.Method.invoke(Unknown Source)
        at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
        at com.install4j.runtime.Launcher.main(Unknown Source)
Caused by: java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
        at sun.awt.HeadlessToolkit.getMenuShortcutKeyMask(Unknown Source)
        at tablet.gui.Tablet.<clinit>(Tablet.java:33)
        ... 6 more
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
        at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
        at java.awt.Window.<init>(Unknown Source)
        at java.awt.Frame.<init>(Unknown Source)
        at java.awt.Frame.<init>(Unknown Source)
        at javax.swing.JFrame.<init>(Unknown Source)
        at com.exe4j.runtime.util.InternalErrorFrame.<init>(Unknown Source)
        at com.exe4j.runtime.LauncherEngine.handleFailure(Unknown Source)
        at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
        at com.install4j.runtime.Launcher.main(Unknown Source)
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
        at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
        at java.awt.Window.<init>(Unknown Source)
        at java.awt.Frame.<init>(Unknown Source)
        at java.awt.Frame.<init>(Unknown Source)
        at javax.swing.JFrame.<init>(Unknown Source)
        at com.exe4j.runtime.util.InternalErrorFrame.<init>(Unknown Source)
        at com.exe4j.runtime.LauncherEngine.handleFailure(Unknown Source)
        at com.exe4j.runtime.LauncherEngine.launch(Unknown Source)
        at com.install4j.runtime.Launcher.main(Unknown Source)
java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
Exception in thread "main" java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
        at java.awt.GraphicsEnvironment.checkHeadless(Unknown Source)
        at java.awt.Button.<init>(Unknown Source)
        at com.install4j.runtime.util.MessageBox.addChoice(Unknown Source)
        at com.install4j.runtime.util.MessageBox.addChoice(Unknown Source)
        at com.install4j.runtime.ErrorHandler.displayGuiErrorMessage(Unknown Source)
        at com.install4j.runtime.ErrorHandler.reportError(Unknown Source)
        at com.install4j.runtime.Launcher.main(Unknown Source)

[imilne]

That looks like you don't have x-windows. Do you?

Iain

[Adamo]

That's because of the way BAM files work - they're designed so you can just peek at small parts of a massive data set without having to load everything into memory, but that means you don't know how many reads are associated with a contig unless you read all of it.

...

You can either search for a read by name, or use the "Jump To" option to move the display to a given location.

Iain

Ok, I didn't know how a BAM file worked... I understand now, sorry for the question.
I'll follow your advices. An ACE file seems appropriate for the data i'm interested in.

[imilne]

Ok, I didn't know how a BAM file worked... I understand now, sorry for the question.
I'll follow your advices. An ACE file seems appropriate for the data i'm interested in.

It's one of the areas where Tablet problem isn't very clear. We're hoping to make some improvements for the next version.

As for comments or questions, they're always appreciated by us, no matter how trivial they may seem. Often it's the only way we know we're doing things right (or not!)

Iain