[litali]

features import doesn't work

I try to upload features for the ACE file, but no features are uploaded ( I choose th gff file, but nothing happens...)

[maubp]

Saw this near the top, and wanted to say that I absolutely love Tablet. Fast and nice to look at, what more could you want.

I'd ask for better display of insertions in SAM/BAM format (the Tablet team are looking at this)

See also this review, which picks up on insertions as a weakness in Tablet:
http://jermdemo.blogspot.com/2010/08...-reviewed.html

Looks like the brand new Tablet release adds both paired end support and improved insertion display in SAM/BAM !

(Its just a shame the SCRI website is having connectivity issues today - I guess they'll be posting an announcement here later this afternoon if they can get back online)

[maubp]

Saw this near the top, and wanted to say that I absolutely love Tablet. Fast and nice to look at, what more could you want.

I'd ask for better display of insertions in SAM/BAM format (the Tablet team are looking at this)

See also this review, which picks up on insertions as a weakness in Tablet:

http://jermdemo.blogspot.com/2010/08/ngs-viewers-reviewed.html

[ECO]

Saw this near the top, and wanted to say that I absolutely love Tablet. Fast and nice to look at, what more could you want.

[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

[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]

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

[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.

[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]

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.

[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]

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...?

[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!

[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]

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?