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Old 08-28-2012, 12:00 PM   #101
deepthi
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Default problem in @SQ lines

Quote:
Originally Posted by agc View Post
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
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Old 08-28-2012, 11:50 PM   #102
TiborNagy
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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.
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Old 08-29-2012, 09:14 AM   #103
deepthi
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Thank you.
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Old 08-30-2012, 12:39 AM   #104
jkbonfield
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Quote:
Originally Posted by TiborNagy View Post
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. :-)
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Old 08-30-2012, 01:29 AM   #105
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Would like to see a version that works in an android tablet
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Old 08-30-2012, 03:18 AM   #106
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Quote:
Originally Posted by ymc View Post
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.

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Old 09-03-2012, 07:09 AM   #107
The Snow
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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
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Old 09-03-2012, 07:16 AM   #108
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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.

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Old 10-03-2012, 07:27 AM   #109
Dolphin22
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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.
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Old 10-03-2012, 08:08 AM   #110
maubp
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Quote:
Originally Posted by Dolphin22 View Post
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).
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Old 10-03-2012, 02:27 PM   #111
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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
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Old 05-02-2013, 12:17 AM   #112
GStephen
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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.
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Old 05-07-2013, 10:12 AM   #113
akshaya.ramesh
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Default 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?
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Old 05-07-2013, 12:58 PM   #114
maubp
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Quote:
Originally Posted by akshaya.ramesh View Post
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/he...lization.shtml
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Old 05-08-2013, 12:59 AM   #115
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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 tablet@hutton.ac.uk

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Old 05-08-2013, 05:14 AM   #116
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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
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Old 07-02-2014, 11:03 AM   #117
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Default 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.
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Old 07-02-2014, 11:25 AM   #118
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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.
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Old 07-03-2014, 12:03 AM   #119
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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...
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Old 07-03-2014, 12:39 AM   #120
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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.
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