[sklages]

I was wondering if it would be possible to show IUPAC codes in consensus.
As I frequently use MIRA to assemble EST datasets, I'd prefer the correct IUPAC code over '?' in the consensus ;-)

cheers,
Sven

[imilne]

Would it be possible to implement some sort of features track to make it easier to see pileups over exons, etc?

We actively working on that, but it's tricky and time consuming unfortunately, and there isn't much demand for it from people in my group. Tablet is an assembly viewer, and to turn it into a genome browser (which I think it would have to be to display the features properly) isn't something we can really commit to.

Attached, however, is a sneak preview of what we do have working in one of the builds. At best it'll be one feature "type" per track. If stuff overlaps then that'll be tough luck - for this version at least

Iain

[imilne]

I was wondering if it would be possible to show IUPAC codes in consensus.
As I frequently use MIRA to assemble EST datasets, I'd prefer the correct IUPAC code over '?' in the consensus ;-)

In the short term, it's unlikely. One of Tablet's original optimizations was to create its own internal alphabet of supported characters. This alphabet was purposely designed to be tiny, mainly so it wouldn't use up much memory. All raw data is translated into a compressed bytestream version of this, allowing us to display data very very quickly. When we moved to caching data on disk, we thought maybe it wouldn't be needed any more, but it turns out it was still useful because the amount of data we need to read and write to disk is subsequently much smaller too (and therefore aids creation/retrieval time), meaning the overhead of using a hard drive over memory isn't that bad.

So for now, we're locked into the way we currently do things, with an alphabet that can't support much more than the basic set of A, C, G, T, and some others we use to help speed up rendering. Ultimately it's currently limited to 16 characters (2^4).

I'm told (correct me if I'm wrong) that MIRA is one of few assemblers that even outputs ambiguity codes, and even then it can be told not to?

Iain

[sklages]

I'm told (correct me if I'm wrong) that MIRA is one of few assemblers that even outputs ambiguity codes, and even then it can be told not to?
Iain

Yes, it is one of the assemblers that does ... but that's not a drawback but a feature, especially for denovo cDNAs assemblies without reference ...

thanks,
Sven

[agc]

SAMSequenceDictionary

Hi,

While attempting to view a sorted BAM file (that has been indexed) with a fasta reference on Tablet, I receive the following error:

java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequence dictionary

Any ideas on what the problem might be?

[imilne]

Hi,

While attempting to view a sorted BAM file (that has been indexed) with a fasta reference on Tablet, I receive the following error:

java.lang.IllegalArgumentException: Cannot add sequence that already exists in SAMSequence dictionary

Any ideas on what the problem might be?

That's not one of our errors, so it must be from Picard, the API we use to read BAM files. It probably means there's something wrong with the underlying BAM file itself, or something about it that Picard can't handle. You might be able to confirm by trying one of the other Java viewers - if you get the same error, it'll be the file; if you don't, then maybe it is Tablet that's at fault.

Someone on the Picard or samtools mailing lists may also be able to help further (or will hopefully read this)...

Iain

[agc]

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!

[Adamo]

Hi,

Tablet gives me the following error message while trying to load a sorted bam file and its corresponding genome:

java.lang.Exception: java.lang.RuntimeException: SAM validation error: ERROR: Record 9187, Read name SRR033843.58925, Zero-length read without CS or CQ tag

Do you know where it can come from?
I've aligned reads with Blat, used pls2sam and processed the file with samtools.

I wonder why *this* read in particular...?

[imilne]

SAM validation error: ERROR: Record 9187, Read name SRR033843.58925, Zero-length read without CS or CQ tag

Do you know where it can come from?

I'll leave this one for the assembler/SAM experts.

With Tablet we've always felt it best to leave these kinds of errors in rather than have it ignore the reads. That way you can be informed when there's something (potentially) not right with the data.

Iain

[Adamo]

Thank you anyway.

This problem happens with all the reads, not only the one mentionned. It may be psl2sam or Blat which causes this error.

[orcy]

have you had a look at the actual record compared to the others?

samtools view bam.file | grep recordName | less

and compare it to a few other reads

samtools view bam.file | less

perhaps there's a missing tab, or an extra endline character?

[Adamo]

Hi,

Tablet gives me the following error message while trying to load a sorted bam file and its corresponding genome:

java.lang.Exception: java.lang.RuntimeException: SAM validation error: ERROR: Record 9187, Read name SRR033843.58925, Zero-length read without CS or CQ tag

Do you know where it can come from?
I've aligned reads with Blat, used pls2sam and processed the file with samtools.

I wonder why *this* read in particular...?

I'll leave this one for the assembler/SAM experts.

With Tablet we've always felt it best to leave these kinds of errors in rather than have it ignore the reads. That way you can be informed when there's something (potentially) not right with the data.

Iain

I have resolved the problem. It was caused by the absence of the corresponding sequences of the matches in the sam file converted from psl. And as Tablet doesn't represent a read without its sequence...
I've been given a script that associate the sequence of a read with its hit (it outputs a bam file, the input is the sam file produced from the psl), if someone need it, feel free to ask.

[imilne]

We now have a version of Tablet that contains visual support for paired-end data (from SAM/BAM files), both in packed and stacked views.

It's not quite ready for release yet, but if anyone wants to give it a try - and is willing to provide us feedback if it doesn't work (!) - then get in touch with us at [email protected] and I can send you details on how to download it. This version also contains some support for rendering GFF data too (annotation tracks basically).

Iain

[Zigster]

how is the work going with indels?
I tried to load up some bwa alignments in which there were insertions in the reads (or maybe deletions in the reference) and everything looked messed up.

[imilne]

how is the work going with indels?
I tried to load up some bwa alignments in which there were insertions in the reads (or maybe deletions in the reference) and everything looked messed up.

Send us an email with the details (and a screenshot) and we'll look into it.

Iain