[maubp]

Yes, I'm using maf2sam.py for the conversion and I had noticed that there was currently no implicit paired-end distance set in the SAM file (Tablet reports all the lengths as 0). I'd be happy to share some MIRA assemblies if it would help, but it seems that this type of shading is beyond Tablet's functionality (at least for the time being).

Please get in touch via a DM on the forum, or via a github message. Or, if you don't mind having it public, posting a URL here would also suit me.

Also, as far as I can see (and please let me know if there something I'm missing), Tablet doesn't differentiate in-contig with off-contig mapped pairs by color, only those with unmapped pairs.

Um. Gordon? I know there are at least four colours in that mode... Maybe room for one more?

Peter

[GStephen]

Um. Gordon? I know there are at least four colours in that mode... Maybe room for one more?

I'm working on it as we speak. It's likely there will be two extra colours as opposed to one though. One for first in pair with its partner in another contig and another for second in pair with its partner in another contig.

Gordon

[maubp]

I'm working on it as we speak. It's likely there will be two extra colours as opposed to one though. One for first in pair with its partner in another contig and another for second in pair with its partner in another contig.

Perhaps it would be more general to use these new colours for reads where the 0x02 "properly paired" flag is not set? That should cover this situation (mapped to different contigs) and things like mapped in the wrong orientation. Assuming the tool generating the SAM/BAM file uses the flag properly

[Certainly this should work with maf2sam.py which currently sets the properly paired flag when the reads are mapped to the same contig]

[phatjoe]

Hi,
I am new to tablet and I've encountered this problem.

error: java.io.IOException: No space left on device

Reference genome file: 1.7Gb
sam file: 35Gb

I have alllocated a 48Gb memory on tablet. Any thoughts on why am I still getting this error?

Thanks in advance!

[imilne]

Hi,
I am new to tablet and I've encountered this problem.

error: java.io.IOException: No space left on device

That sounds like you're out of disk space rather than memory. Go into Tablet Options and change the location of its cache directory to somewhere with plenty of free space. If you also convert the sam file to bam, then Tablet won't need much working space either.

Iain

[phatjoe]

That sounds like you're out of disk space rather than memory. Go into Tablet Options and change the location of its cache directory to somewhere with plenty of free space. If you also convert the sam file to bam, then Tablet won't need much working space either.

Iain

You are right! Thanks for the speedy reply!

[GStephen]

We've released a new version of Tablet today. People with Tablet already installed should see the update prompt the next time they open Tablet.

You can download Tablet from our website where there is also a listing of the changes to Tablet since the last release.

Gordon

[zlu]

It already can. Just right-click the consensus sequence and select a copy-to-clipboard option.

Iain

When I select the copy-to-clipboard option, the sequence that gets copied is in fact the reference sequence. So is the consensus here not referring to the real consensus of the mapping? In the attached screen-shot, I'll say the highlighted T should be the consensus but not the C that shows up in the "consensus" track. Or am I doing something wrong here?

[maubp]

When I select the copy-to-clipboard option, the sequence that gets copied is in fact the reference sequence. So is the consensus here not referring to the real consensus of the mapping? In the attached screen-shot, I'll say the highlighted T should be the consensus but not the C that shows up in the "consensus" track. Or am I doing something wrong here?

I don't think Tablet attempts to calculate a "consensus" from the reads, it just shows you the reference sequence they are mapped against.

If you are looking at a de novo assembly file, then this "reference" would be the consensus as calculated by the assembly tool.

i.e. There isn't a "consensus" track in Tablet.

[zlu]

...
i.e. There isn't a "consensus" track in Tablet.

That's what I thought. Thanks for the clarification.

By the way, does anyone know of a "simple window-based" program (for the lab people ) that is capable of calculating the consensus from a mapping project?

[Crypticfortune]

By the way, does anyone know of a "simple window-based" program (for the lab people ) that is capable of calculating the consensus from a mapping project?

As long as by "window-based" you mean a GUI and not MS Windows I'd recommend you try out Samscope. It will show you an "estimated" consensus for the bases you're looking at. I say "estimate" because if you have more reads than pixels on a given base, it might ignore some of them in said estimate (if you scroll around and display all of them at least once, they will all be included). This isn't really the point of Samscope, so I figure an estimate is good enough, but if there's actually demand for this sort of thing, it wouldn't be too hard to force exact calculation, on say mouse over or something. So easy, I think I'll go add that feature now in fact...

[schmima]

hm - interesting viewer. However - I did not install it yet as I generally don't like to execute some kind of installer where I have no clue what it does where. I wonder if there are any command-line options that may be of interest to me or if I can find somewhere some information about it?

[Crypticfortune]

hm - interesting viewer. However - I did not install it yet as I generally don't like to execute some kind of installer where I have no clue what it does where. I wonder if there are any command-line options that may be of interest to me or if I can find somewhere some information about it?

*Edit* Doh, that question was from a different user, not zlu. Totally embarassing. Sorry!

I don't want to hijack this Tablet thread over another viewer, so feel free to contact me directly or use the samscope sourceforge site, or start another thread here or something, if you have questions. But for now, you can use "scons --dry-run" to show what any scons command *would* do without actually doing it (like "scons install --dry-run"). Or you can just run it from the build directory without installing it. The samscope wiki has some more details on building and installing.

[schmima]

Ups - I'm sorry. With the "interesting viewer" I was referring to tablet - not samscope.

[arvid]

hm - interesting viewer. However - I did not install it yet as I generally don't like to execute some kind of installer where I have no clue what it does where. I wonder if there are any command-line options that may be of interest to me or if I can find somewhere some information about it?

If you install it as a normal user (which works fine with Tablet for me) you don't have to worry - there is an uninstaller as well. I wouldn't install any unknown software as root, agreed!