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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.
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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. -
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.Comment
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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.Comment
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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.Comment
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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.
IainOur software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALiComment
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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.Last edited by seq_GA; 06-22-2010, 12:20 AM.Comment
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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.Originally posted by seq_GA View Post
IainOur software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALiComment
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Thx Iain..Comment
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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:
How to overcome this? Sorry for asking too many questions. Thanks.Code:An error has occurred while attempting to open the provided assembly. java.lang.NullPointerException Input file(s) used: http:/qyz03/misc/test.bam
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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.
IainOur software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALiComment
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Thank you so much Iain for your help. I have missed something in the url and now I am able to load.Comment
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Yes, I missed one slash in the url.
The correct url isAnd 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.Code:http://qyz03/misc/test.bam
Code:Unfortunately, Tablet no longer has enough memory to complete its current task and must be closed.
Last edited by seq_GA; 06-22-2010, 12:56 AM.Comment
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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