[Dolphin22]

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.

[imilne]

I'm not quite sure what you're asking, but Tablet needs an index file to read a BAM file. If you haven't got one, then you need to create one with samtools.

Iain

[The Snow]

Hello,

I have the following problem using Tablet. When I import bam files sorted with samtools (I understood that .bai seems to be mandatory) I do not have any issue.
However when I try to import a .bam files created with bamtools that contains ONLY the aligned sequenced, Tablet gave me a java error. I think that the problem is related to the bai file (bamtools does not create a .bai when extract only the aligned reads). Isn't it? Is there a way to import just the reads aligned created with bamtools?

Thank you!

Fabio

[imilne]

Would like to see a version that works in an android tablet

Don't think we haven't already thought of that

Tablet was actually named - like most of our software - after an item of food, although we're in real tooth-rot territory here: http://scruss.com/tablet.html

Tablet also used to play a mean game of Breakout using your data, but unfortunately that code is broken just now and we haven't gotten around to fixing it again. Minesweeper can still be played in Flapjack though.

Iain

[ymc]

Would like to see a version that works in an android tablet

[jkbonfield]

You can easily remove duplicated header elements:
samtools view -H input.bam | uniq >header.txt
After that extract body:
samtools view input.bam >body.txt

And create a new bam file:
cat header.txt body.txt | samtools view -S -b - >new.bam

If the @SQ tags are not near, use ReorderSam from Picard.

As a brief aside, I tend to use pipes for these sort of things to improve caching and avoid temporary files. Eg

(samtools view -H input.bam | uniq; samtools view input.bam ) | samtools view -S -b - > new.bam

The use of bracketting to create subshells and join the output together again before piping is a very useful trick.

Programs that don't support pipes can often be fooled via use of FIFOs (mknod p or mkfifo) provided they don't seek. Bash even has some cryptic >(cmd) and <(cmd) syntax to hide it all away too. :-)

[deepthi]

Thank you.

[TiborNagy]

You can easily remove duplicated header elements:
samtools view -H input.bam | uniq >header.txt
After that extract body:
samtools view input.bam >body.txt

And create a new bam file:
cat header.txt body.txt | samtools view -S -b - >new.bam

If the @SQ tags are not near, use ReorderSam from Picard.

[deepthi]

problem in @SQ lines

Yes, there was a problem with the BAM file - several sequence names were left blank (due to my reference fasta file including a space between the '>' sign and the sequence name - IE '> chr07' instead of '>chr07'), and therefore were seen as duplicates.

Thanks!

Hi ,
What did you do to clean your bam file?
I also have problem of duplicate lines in @SQ lines of bam header. Because of that I can not add Read groups to bam file.
Please help me?

Deeps

[arvid]

Actually, now that you mention it, Tablet does also create some settings files that go in a folder called .scri-bioinf (in your home folder). But they pretty much have to go there because we can't be sure the install folder is writable (eg Program Files on Windows with UAC, etc).

I don't mind the ".<software>" folders, that's standard, as long as your updater (or the software itself) also makes sure to upgrade existing user settings, if needed for a newer version, and doesn't just overwrite them.

[imilne]

Did you consider either feeding Tablet into major Linux repositories or hosting your own repositories for the major Linux distributions?

It's one of those "would be nice to have, but we haven't the time to do it" things unfortunately. The last time I checked, 30% of Tablet's users are on Linux, so it's certainly a good chunk of people it could benefit. (The rest are 50% Windows, 20% OS X in case anyone was wondering).

What I mean with "ugly folder structure" is when quick-hack-scripts (I'm not referring to Tablet here) create all sorts of folders for "databases", "user files", "downloaded files" etc. (usually with non-locale-aware names) in the home directory.

Actually, now that you mention it, Tablet does also create some settings files that go in a folder called .scri-bioinf (in your home folder). But they pretty much have to go there because we can't be sure the install folder is writable (eg Program Files on Windows with UAC, etc).

Iain

[schmima]

@ imilne

I would not say, that I don't like automated installation - I just like to know before starting a script, what it will try to do and if I have to pass on some configuration arguments on the command line.

In your case the installer is perfectly fine - but as you said - this is rather an exception than a rule.

* edit
@ arvid
yep - that's exactly what I meant with the ugly folder structure

[arvid]

So what constitutes an 'ugly' folder structure then? Tablet creates just one top-level folder, called funnily enough, Tablet. Whether you put that in your home folder (non root user) or somewhere else on your file system (as root) is entirely up to you. As far as I'm aware, the only other files the installer creates relates to the shortcuts/symlinks. It's made with install4j, and is certainly *not* a quick-hack script.

The installer application allows us to build bundles for all platforms with the minimum of fuss, and also bundle Java too which massively reduces the burden on your 'average' user. Other than using a bit more disk space (a non issue with today's hard drives), that Java doesn't interfere with any other version that might be on your system. And bar one or two exceptions, our end users generally haven't had a problem getting Tablet installed and running. In my experience that's pretty rare in the world of bioinformatics, where quick-hack scripts are often the order of the day.

Iain

The ugly-folder stuff wasn't about Tablet, actually I don't mind the Tablet installer at all. I wish more bioinformatic software came with installer packages, or even better would be supplied through repositories (and thus could be updated in a coordinated fashion on standard OS distributions). Did you consider either feeding Tablet into major Linux repositories or hosting your own repositories for the major Linux distributions?

What I mean with "ugly folder structure" is when quick-hack-scripts (I'm not referring to Tablet here) create all sorts of folders for "databases", "user files", "downloaded files" etc. (usually with non-locale-aware names) in the home directory.

[imilne]

When those come from the typical, trusted repositories, they don't create ugly folder structures, because they don't need to (they know where to put things) - quick-hack installer scripts tend to to create such ugly folder structures inside user folders, though...

So what constitutes an 'ugly' folder structure then? Tablet creates just one top-level folder, called funnily enough, Tablet. Whether you put that in your home folder (non root user) or somewhere else on your file system (as root) is entirely up to you. As far as I'm aware, the only other files the installer creates relates to the shortcuts/symlinks. It's made with install4j, and is certainly *not* a quick-hack script.

The installer application allows us to build bundles for all platforms with the minimum of fuss, and also bundle Java too which massively reduces the burden on your 'average' user. Other than using a bit more disk space (a non issue with today's hard drives), that Java doesn't interfere with any other version that might be on your system. And bar one or two exceptions, our end users generally haven't had a problem getting Tablet installed and running. In my experience that's pretty rare in the world of bioinformatics, where quick-hack scripts are often the order of the day.

Iain

[arvid]

So you don't like RPMs or apt bundles either then?

Iain

When those come from the typical, trusted repositories, they don't create ugly folder structures, because they don't need to (they know where to put things) - quick-hack installer scripts tend to to create such ugly folder structures inside user folders, though...