Tablet visualization tool for linux

[seq_GA]

Hi, I have downloaded tablet_linux_x64_1_10_05_21.sh and installed in our linux server. Do I need to use X-win to visualise the data (in linux server) from my desktop. Please let me know the steps involved. I have bam file from illumina reads (human). What are the other files needed for visualisation? Thanks.

[Jose Blanca]

You can open x applications remotely in several ways. A very easy one is to use the X server network capabilities. ssh into the server doing:

ssh -X -C server.net

Now when you open an X application like xeys the application will show up in your client machine.

[seq_GA]

Hi Jose,
Thx for the response. Can you please be bit more clear as I don't understand. For example if my linux server name is G001, do I have to do as below from the my desktop (windows cmd prompt) C:\Program Files\SSH Communications Security\SSH Secure Shell>ssh2.exe -X -C seqGA@GA001?

I am still not getting the visualzation screen from my desktop. I have installed Tablet in my linux server. Thanks.

[sklages]

As alternative you might want to download the Windows 32bit or 64bit version of tablet and install it locally on your Windows PC, so you don't need to access the program via the network.

[Jose Blanca]

The instructions I gave you will only work from a linux machine, you need a X server.
Another alternatives are:
- Xming. hard, but free.
- nx. Easy but non free.

[seq_GA]

Hi all,
Thx for the response. Since I don't want to import bam files from the server into my desktop every time, I am working on making xwin32 to work..Thx again.

[imilne]

If you can network map to the BAM files from your windows desktop (or put the files on a web server running on the linux box), then it won't really matter. Tablet (and any of the graphical viewers) will let you look at the BAM file without having to copy the whole thing to your local system.

Iain

[seq_GA]

Thx Ian for the help. I will definitely try.
we have the bam files on a web server running on linux box. How to use Tablet in that case. I am downloading the windows version to try the next step. Thanks.

[imilne]

we have the bam files on a web server running on linux box. How to use Tablet in that case.

Just get the URL of the file on the clipboard (eg http://someserver/somefile.bam) and paste that into the Open Assembly dialog within Tablet. Same with the reference data if it's on the server too.

Iain

[seq_GA]

Thx Iain..

[seq_GA]

Hi Iain,

When I try pasting the below url as http:/qyz03/misc/test.bam in the primary assembly file or URL, the Reference/consensus file or URL becomes inactive and when I click open button, I get to see the following error:

An error has occurred while attempting to open the provided assembly. 
java.lang.NullPointerException

Input file(s) used:
http:/qyz03/misc/test.bam

How to overcome this? Sorry for asking too many questions. Thanks.

[imilne]

Check that your web browser will attempt to download the file if you paste the URL in that.

And also attach a copy of the "output.log" file from Tablet's install dir. It might give me a clue as to what's going wrong.

Iain

[seq_GA]

Thank you so much Iain for your help. I have missed something in the url and now I am able to load.

[imilne]

Thank you so much Iain for your help. I have missed something in the url and now I am able to load.

Was it just simply a wrong URL? I'll need to check what Tablet is doing if that happens as that wasn't exactly the world's best error message for such a simple mistake

[seq_GA]

Yes, I missed one slash in the url.

The correct url is

http://qyz03/misc/test.bam

And now I see another problem. After loading the bam file, I concatenated all fasta files of human genome into hg18.fa and try uploding and I see the following error message.

Unfortunately, Tablet no longer has enough memory to complete its current task and must be closed.