SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
PubMed: A biologist's guide to de novo genome assembly using next-generation sequence Newsbot! Literature Watch 0 01-10-2012 12:10 PM
Tablet assembly viewer valei Bioinformatics 2 03-07-2011 07:09 AM
problem of viewing assembly data in Tablet percy Bioinformatics 4 09-15-2010 06:42 AM
Tablet visualization tool for linux seq_GA Bioinformatics 19 06-22-2010 01:35 AM
Tablet Next Generation Sequence Assembly Visualization mbayer Literature Watch 0 01-12-2010 06:43 AM

Reply
 
Thread Tools
Old 07-16-2010, 07:33 PM   #41
orcy
Junior Member
 
Location: Brisbane

Join Date: Jan 2010
Posts: 8
Default

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

Code:
samtools view bam.file | grep recordName | less
and compare it to a few other reads

Code:
samtools view bam.file | less
perhaps there's a missing tab, or an extra endline character?
orcy is offline   Reply With Quote
Old 07-19-2010, 01:22 AM   #42
Adamo
Member
 
Location: Paris

Join Date: Jun 2010
Posts: 28
Default

Quote:
Originally Posted by Adamo View Post
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...?
Quote:
Originally Posted by imilne View Post
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.

Last edited by Adamo; 07-19-2010 at 01:26 AM.
Adamo is offline   Reply With Quote
Old 08-12-2010, 07:21 AM   #43
imilne
Member
 
Location: JHI, Dundee, UK

Join Date: Jan 2010
Posts: 68
Default

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 tablet@scri.ac.uk 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
__________________
Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi
imilne is offline   Reply With Quote
Old 08-12-2010, 07:25 AM   #44
Zigster
(Jeremy Leipzig)
 
Location: Philadelphia, PA

Join Date: May 2009
Posts: 116
Default

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.
__________________
--
Jeremy Leipzig
Bioinformatics Programmer
--
My blog
Twitter
Zigster is offline   Reply With Quote
Old 08-14-2010, 10:05 AM   #45
imilne
Member
 
Location: JHI, Dundee, UK

Join Date: Jan 2010
Posts: 68
Default

Quote:
Originally Posted by Zigster View Post
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
__________________
Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi
imilne is offline   Reply With Quote
Old 08-14-2010, 02:49 PM   #46
ECO
--Site Admin--
 
Location: SF Bay Area, CA, USA

Join Date: Oct 2007
Posts: 1,358
Default

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.
ECO is offline   Reply With Quote
Old 08-30-2010, 12:23 PM   #47
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

Quote:
Originally Posted by ECO View Post
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
maubp is offline   Reply With Quote
Old 09-10-2010, 03:42 AM   #48
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

Quote:
Originally Posted by maubp View Post
Quote:
Originally Posted by ECO View Post
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 is offline   Reply With Quote
Old 09-10-2010, 07:54 AM   #49
litali
Member
 
Location: us

Join Date: Jul 2010
Posts: 78
Default 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...)
litali is offline   Reply With Quote
Old 09-10-2010, 08:11 AM   #50
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

Quote:
Originally Posted by litali View Post
I try to upload features for the ACE file, but no features are uploaded ( I choose th gff file, but nothing happens...)
The table on the left has three tabs: Contigs, Features, Search. Switch to Features and you should see something assuming it worked.
maubp is offline   Reply With Quote
Old 09-10-2010, 09:49 AM   #51
sjackman
Member
 
Location: Vancouver, Canada

Join Date: Mar 2009
Posts: 15
Default

Quote:
On a related note, what is the position on reads which extend beyond the reference sequence at the start or end of the sequence. The Picard API in particular doesn't seem to like reads which either start before the reference sequence, or end after it. Are these reads valid in SAM/BAM or not?
To support de novo assembly, I find it very useful to be able to place reads before or after the reference sequence, primarily to show that a particular contig can be extended further by reads.

I believe the standard is to soft clip reads that extend past the reference, but if the read is placed entirely past the reference so that not a single base overlaps, I'm not sure what to do.

Cheers,
Shaun

Last edited by sjackman; 09-10-2010 at 12:52 PM.
sjackman is offline   Reply With Quote
Old 09-10-2010, 09:56 AM   #52
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

Quote:
Originally Posted by sjackman View Post
To support de novo assembly,...
Interesting post, but was it in the wrong thread?
maubp is offline   Reply With Quote
Old 09-10-2010, 12:39 PM   #53
sjackman
Member
 
Location: Vancouver, Canada

Join Date: Mar 2009
Posts: 15
Default

I responded to this posting earlier in this thread:
http://seqanswers.com/forums/showpost.php?p=14732

Cheers,
Shaun

Last edited by sjackman; 09-10-2010 at 12:53 PM.
sjackman is offline   Reply With Quote
Old 09-10-2010, 01:07 PM   #54
sjackman
Member
 
Location: Vancouver, Canada

Join Date: Mar 2009
Posts: 15
Default

Quote:
As usual, it should auto-update the next time you run it, or you can grab the download manually from http://bioinf.scri.ac.uk/tablet
This web site appears to be down. Is this a temporary problem?

Cheers,
Shaun
sjackman is offline   Reply With Quote
Old 09-10-2010, 10:24 PM   #55
litali
Member
 
Location: us

Join Date: Jul 2010
Posts: 78
Default

Quote:
Originally Posted by maubp View Post
The table on the left has three tabs: Contigs, Features, Search. Switch to Features and you should see something assuming it worked.
I do switch to features, but there are 0 features there...
litali is offline   Reply With Quote
Old 09-11-2010, 03:11 AM   #56
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,542
Default

Quote:
Originally Posted by sjackman View Post
This web site appears to be down. Is this a temporary problem?
The whole of the SCRI website is down - they're cut off, probably until Monday now.
maubp is offline   Reply With Quote
Old 09-13-2010, 01:03 AM   #57
GStephen
Junior Member
 
Location: Dundee, UK

Join Date: Mar 2010
Posts: 9
Default

Quote:
Originally Posted by litali View Post
I do switch to features, but there are 0 features there...
The most common reason for features not showing up is that the contig/reference names in the GFF file don't match what's loaded into Tablet. Try having a look at and potentially altering the contig / reference names in the GFF file and the features should load with no problems.
GStephen is offline   Reply With Quote
Old 01-25-2011, 05:00 AM   #58
imilne
Member
 
Location: JHI, Dundee, UK

Join Date: Jan 2010
Posts: 68
Default

I keep forgetting to post updates on Tablet here, so I'll try to make more of an effort for 2011

Here's a summary of the changes in today's (25th Jan) release:

- NEW: Various improvements to the pair-matching code should result in much faster loading of paired-end data.
- NEW: Drawing paired-reads that include "link lines" is now faster.
- NEW: Added new right-click options to the main canvas that provides several export-to-disk options for reads.
- NEW: Added a "Visible Reads" tab, that displays a dynamically changing table of all on-screen reads as you navigate around a contig.
- NEW: Added CTRL/CMD mousewheel zooming to the main canvas.
- CHG: Altered the SAM parsing code to better handle files which have been produced by tools which haven't adhered to the SAM specification.
- CHG: Rearranged some of existing options on the main canvas's right-click menu.
- CHG: Changed to a different SQLite binary for use on OS X that allows it to work on all systems (10.4, 10.5, 10.6) again.
- BUG: Fixed some installer problems that were causing issues on Ubuntu Linux.

As usual, Tablet should auto-update the next time you run it, or you can grab the download manually from http://bioinf.scri.ac.uk/tablet

Iain
__________________
Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi
imilne is offline   Reply With Quote
Old 03-30-2011, 09:36 AM   #59
Guidobot
Junior Member
 
Location: San Diego

Join Date: Jan 2011
Posts: 8
Default

Just wanted to say that I really appreciate Tablet. In particular, Tablet works great with text [alignment] file formats, e.g. SAM and MAQ .map.txt.

I am working on a very low-end system (1GHz, <2Gb RAM) and have had problems using other alignment viewers and/or various tools required to create necessary [supporting] file formats (e.g. maqindex, samtools sort).

To add a very minor constructive criticism for the author's consideration: I found the read search (by ID) unusably slow, which was a surprise since for my queries and input files a simple unix 'grep' took less than 1 second.

I look forward to any future developments, especially for (de novo) SNP annotation and repeat masking (which can affect the coverage statistics depending on the mapping software used).

Last edited by Guidobot; 03-30-2011 at 09:39 AM. Reason: readability
Guidobot is offline   Reply With Quote
Old 03-30-2011, 09:53 AM   #60
imilne
Member
 
Location: JHI, Dundee, UK

Join Date: Jan 2010
Posts: 68
Default

Quote:
Originally Posted by Guidobot View Post
Just wanted to say that I really appreciate Tablet. In particular, Tablet works great with text [alignment] file formats, e.g. SAM and MAQ .map.txt.
Thanks for the comments. Always nice to hear

Quote:
Originally Posted by Guidobot View Post
To add a very minor constructive criticism for the author's consideration: I found the read search (by ID) unusably slow, which was a surprise since for my queries and input files a simple unix 'grep' took less than 1 second.
Can you send us any sample files (to tablet (at) scri.ac.uk)? Sounds like something isn't quite right...

Iain
__________________
Our software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi
imilne is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:58 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO