[imilne]

First off the "pos=" value does not match the same starting position displayed in Tablet but is off by 1.

Yep, that one's a bug (and has already been fixed), so it'll be in the next release.

Beyond that I'm curious what it does with insertions.

What kind of? CIGAR ones?

Iain

[m_welkers]

Exporting reads intersecting column

Just want to say, I really like tablet and use it frequently! I do have some quick questions. I work with influenza datasets and when I load in my datasets to look for SNP's, I go to that position in Tablet and export all the reads that intersect that column. The reads are exported to a file in a .fas format and I noticed a few things. First off the "pos=" value does not match the same starting position displayed in Tablet but is off by 1. (So in Tablet start position of the read is 2155 and exported it says pos=2154. The CIGAR string is 54M so no padding or other issues with the string.)

Beyond that I'm curious what it does with insertions. It doesn't appear to display them in the read so it doesn't extract the sequence directly from the reads in the alignment file. How does it "make" the sequences then?

Ps. Keep up the good work!

[imilne]

What does the new contig. Mismatch value report refer to?

It's a count of the number of read bases (across all reads) that don't match the consensus/reference at that base. It doesn't attempt to do anything clever (because we need to calculate the number very fast), so if a read's base doesn't match the consensus - no matter the reason - then it gets counted.

The decimal places may be rounded for display purposes in the table, but if you right-click it and copy its data to the clipboard, you'll get the full number.

Iain

[Guidobot]

Hi Iain,

I sent you an email and the datasets. I also asked a question that I think would be good to answer here.

What does the new contig. Mismatch value report refer to?

If it is the total number of mismatches w.r.t the consensus/reference across all reads, is there a minimum number/percentage of reads required to denote a difference (i.e. probable SNP)? Does it also include mismatches for reads counted as features (i.e. with INDELs)?

Also the value appears to be rounded (%g) so it is hard to know the decimal point accuracy.

[imilne]

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

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

[Guidobot]

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).

[imilne]

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

[GStephen]

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.

[maubp]

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.

[litali]

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...

[sjackman]

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]

I responded to this posting earlier in this thread:

http://seqanswers.com/forums/showpost.php?p=14732

Cheers,
Shaun

[maubp]

To support de novo assembly,...

Interesting post, but was it in the wrong thread?

[sjackman]

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

[maubp]

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.