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.
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Originally posted by ECO View PostSaw this near the top, and wanted to say that I absolutely love Tablet. Fast and nice to look at, what more could you want.
See also this review, which picks up on insertions as a weakness in Tablet:
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Originally posted by maubp View PostOriginally posted by ECO View PostSaw this near the top, and wanted to say that I absolutely love Tablet. Fast and nice to look at, what more could you want.
See also this review, which picks up on insertions as a weakness in Tablet:
http://jermdemo.blogspot.com/2010/08...-reviewed.html
(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)
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Originally posted by litali View PostI try to upload features for the ACE file, but no features are uploaded ( I choose th gff file, but nothing happens...)
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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?
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,
ShaunLast edited by sjackman; 09-10-2010, 12:52 PM.
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Last edited by sjackman; 09-10-2010, 12:53 PM.
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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
Cheers,
Shaun
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Originally posted by litali View PostI do switch to features, but there are 0 features there...
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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
IainOur software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi
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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).
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Originally posted by Guidobot View PostJust 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.
Originally posted by Guidobot View PostTo 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.
IainOur software: Tablet | Flapjack | Strudel | CurlyWhirly | TOPALi
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