[Zan]

Hi imilne,
I am unable to locate tablet.vmoptions. I have gone through all tablet files and it is not there. Is there another way of allocating memory?

P.S I installed tablet using conda.

[imilne]

The server is offline, which makes tablet unusable. Could you please disable the requirement for loading the update server on startup?
EDIT: the issue can be fixed by referring to a non existing proxy on localhost port 8080...

You can disable checking for updates in the Preferences/Options. I didn't think it would stop it working if the server was offline - I'll check on Monday.

(The server is off due to a full electrical power down at the institute - it should be back at some point today).

[thomasvangurp]

The server is offline, which makes tablet unusable. Could you please disable the requirement for loading the update server on startup?
EDIT: the issue can be fixed by referring to a non existing proxy on localhost port 8080...

[imilne]

Is there any chance of getting Tablet to colour reads based on concordance with the read number, for validating strand-specific sequencing? Something like {(Read1 + Reverse orientation) or (Read2 + forward)} = Red, {(Read2 + Reverse orientation) or (Read1 + forward)} = Green. It's a bit frustrating having read end colouring, or map direction colouring, but not a combination of the two.

I can't see that being a problem. Can you throw the request in an email to [email protected] so we can track it properly, and let you test whatever we come up with.

[gringer]

Is there any chance of getting Tablet to colour reads based on concordance with the read number, for validating strand-specific sequencing? Something like {(Read1 + Reverse orientation) or (Read2 + forward)} = Red, {(Read2 + Reverse orientation) or (Read1 + forward)} = Green. It's a bit frustrating having read end colouring, or map direction colouring, but not a combination of the two.

[imilne]

More likely it's the mismatch column in the contigs list (down the left-hand side), which is simply the percentage of bases across all reads that don't match the reference. This is ordinarily a value for the entire contig, but as it obviously can't calculate that with a BAM file until it actually loads some data, then it only shows the value for the currently loaded chunk (controlled by Tablet's 'window size' option).

As for help, it's all linked to from within Tablet itself. We're going through a period of website redesign just now, and the main site no longer contains any links to it. That'll change once we sort out a few WordPress issues...

[maubp]

I think you are asking about Tablet's option to visually highlight bases in the mapped reads which do not map the reference genome. For this to work, you must load a BAM file with a FASTA reference file. Then there is a slider control on the tool bar (next to the zoom slider) which adjusts the colours. Bases which match the reference are dark, mismatches are bright.

[vanillasky]

Request for Tablet Tutorial

Hi,

I'm trying to use Tablet to visualize a metagenome assembly. I wanted to ask what the mismatch feature is and how it can be used as it was not discussed in your paper. Is there anyway you could work on a manual or tutorial to describe how to use the different features in Tablet? I couldn't find this information in your paper or on your website. A tutorial video or powerpoint description would be more helpful than screenshots.

[akshaya.ramesh]

They are AFG files and I was using paired end data. I did not realize that Tablet does not support PE reads, would you know of another asssembly visualization program that supports AFG and PE data?

Thanks,
Akshaya

[imilne]

They're talking about AFG files, not BAM.

Is there any way you can give us access to the data so we can try to replicate the problem (as I've never seen it with any files we've tried)? Also note that Tablet doesn't support paired-end data with AFG in case you're trying that. You can email us at [email protected]

Iain

[maubp]

It cuts off contigs that are larger in size (all contigs above 20,000 bp are cut-off).

Assuming you are looking at BAM files, this would be the BAM window. You should see a blue 'scroll' bar above the overview pane showing which part of the contig you are viewing. You can also increase the BAM window (at the cost of reduced performance, more memory etc - don't do this for deep coverage files). See:

http://bioinf.hutton.ac.uk/tablet/help/bam-data-visualization.shtml

[akshaya.ramesh]

errors in visualization of velvet.afg files in Tablet

I have been working on de-novo genome assembly using the Velvet algorithm and I am using Tablet to visualize my .afg files.

Of the 10,000 contigs generated in my contigs.fasta file, I am able to visualize only the first 4,000 contigs. My contigs are ordered by size, from the smallest to largest. It cuts off contigs that are larger in size (all contigs above 20,000 bp are cut-off). I have increased the memory allocation in Tablet and have storage left and I am not exactly sure as to what is going on.

Has anyone else run into similar problems?

[GStephen]

Just quickly reviving this thread to let people know that a couple of new versions of Tablet have been released over the last few weeks. As ever existing users should be automatically notified that an update is available.

[orcy]

Bam files don't encode any features, just the reads and the mappings.

Unless you have a feature file for the genome you mapped to, there will be no features. For tablet, I think it needs to be gff3, but I may be wrong, its been a while since I used it. There are tools in the bioperl scripts folder for converting genbank to gff3

[maubp]

Hey

I have a bit of a problem. I already have a bam file and a fai file. How do I load the bam AND the bai file into tablet to have all features?
I just managed to load the bam file without any features.

Assuming the BAM and BAI files are in the same directory, and named appropriately just load the BAM file and the BAI file is found automatically.

If you have example.bam, then the index file should be called example.bam.bai or example.bai (but watch out if your operating system is hiding the extensions from you - Windows does this by default).