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Assembly for differential expression analysis
by Jose Trejo 19 Apr '13

19 Apr '13

Dear Trinity developpers, I have been using the program to assemble the transcriptome of an organism without a good quality genome. The purpose of this transcriptome is to be used for differential expression analysis. Since I wanted the transcriptome to be as complete as possible I relied on high coverage. For my first assembly I used ~1 billion single-end reads, these reads are from different libraries and the length range goes from 25 to 75 bp. After running Trinity I got 320276 contigs longer than 100 bp. As some of the contigs were redundant I decided to used minimus2 to merge very similar sequences, and I ended up with more than 100000 contigs. When I mapped the libraries that I want to analyze for differential expression more than 89 % of the reads per library were mappable and around 1-2 % of the reads were aligning to more than one place, so I was quite happy with these results. I understand that with very high coverage I could be assembling transcripts that originated from pervasive transcription, and I think that this could be one of the reasons why I am getting over 100000 contigs, besides fragmentation. But this might not be a major problem since I could apply filters before proceeding with the differential expression analysis, for example I could only keep contigs that have more than x number of reads. However, now I have access to paired-end libraries and to other single-end libraries that have longer reads (75-100 bp), therefore I assembled these new libraries to check whether paired-end information could solve fragmentation problems. All together I had 2682537009 reads and I used in silico normalization to reduce the number of reads to 107846820. For the normalization I did not used the --PARALLEL_STATS parameter (memomy limitations). I followed the same pipeline than with my first assembly and after Trinity and minimus2 I have 200655 contigs. Nevertheless, now I have more redundant contigs, for instance some components have more than 100 sequences and they are sharing at least 50 bp; and I do not see an evident gain in completeness when I compare my two transcriptomes, at least with the assays that I carried out, such as checking the number and coverage of orthologous sequences that are included in the assemblies, using as reference the transcriptome of the phylogenetically closest organism. At this point I do not know whether it will be better to use my first assembly for further analysis or to try to assemble my new dataset again using options like --REDUCE (as previously suggested http://sourceforge.net/mailarchive/forum.php?thread_name=CAJCu8qPrOE1BjFPk%…) or --max_number_of_paths_per_node to solve redundancy problems and --min_kmer_cov to not include so lowly expressed transcripts. I would appreciate any comments or suggestions on this regard. Regards, Jose Trejo Uribe

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Filer windows
by Roel Wagenaar 19 Apr '13

19 Apr '13

After having upgraded my desktop-system from debian/squeeze to debian/wheezy, and installing trinity from the nightly-builds repository, I now find my filer windows are not showing the names under the icons. Is this a known problem? -- Roel Wagenaar, Linux-User #469851 with the Linux Counter; http://linuxcounter.net/ Antw.: Omdat het de volgorde verstoord waarin mensen tekst lezen. Vraag: Waarom is top-posting een slechte gewoonte? Antw.: Top-posting. Vraag: Wat is het meest ergerlijke in e-mail? Ignorence is when you don't know anything and somebody finds out.

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Kick-Off Launcher
by Alexandre Couture 17 Apr '13

17 Apr '13

Hi everyone! In the trinity-devel mailing list, there is a nst about keeping or removing the Kick-Off launcher. Here is a part of what is written: Timothy Pearson wrote: >> A good solution would be to 1) remove kickoff since it's unlikely that >> it is used, and doesn't keep in the style of trinity and port the cool >> features of kickoff into the original kicker panel, if there are any. > I would need a list of any improvements in Kickoff that are not in Kicker. > Copious amounts of whitespace around each widget is not considered an > improvement. ;-) Perhaps you could gather information from list members > on why they use Kickoff vs. Kicker? > Francois Andriot wrote: >Hello, I'm always using Kickoff menu instead of Kicker, so I would'nt >like it to be removed. >I currently have no problem with it. >Here are some reasons: >- I prefer having separate tabs for favorites/all >applications/Computer/History , instead of having a single huge menu >with many submenus. >- I prefer the search feature of Kickoff, which displays immediatly the >icon of the app I'm searching. In kicker, the search feature justs grays >out the directories, but I still have to browse the tree to find the >application I want. When the application list is very long, it is still >not very convenient. >- I like the way applications are shown in menu: a "big" icon, >application name written with big letters, application summary with >small letters. So there is no confusion between application name and >application summary. >Maybe we should just ship Kickoff as a separate application, like kbfx ? I have the same point of view as Francois Andriot on that and I can even add: -Kick-Off is as fast as though. If the program I want to launch is Gimp, I click on the start menu, I write ''gim'' on the keyboard and a menu with ''Gimp'' already highlighted appear. I just have to press enter. Otherwise, in the classic menu, I would have to find the ''Graphics'' menu and I would need to read all the names of every programs in the list before I can see ''Gimp'' in the list. And everybody here knows that TDE comes with plenty of programs, so depending of what you are looking for, the menu can be long... We use search engines to find what we want on the Web, but it wouldn't be a good idea on your computer? -Having a little summary of what the programs are is much more intuitive than having to start it, to see what it is. It is just more simple for users coming from Windows. -On my little Asus EEE, with a screen resolution of 800x480, the Kick-off is just the right size, where on the classic start menu, often a sub-menu takes all the screen and many columns, and it gets just confusing and harder to find what you are looking for. -I just don't get the point of users telling everywhere on this mailing list that NOTHING should change in TDE incomparison with KDE 3.5.10 and every single bit should stay identical, but the Kick-Off should be dropped. It is the same thing with Dolphin. Those are 2 KDE3 programs, it is not because they also exists in KDE4 that they are evil. If the Kick-Off is to be dropped one day or another, would it be at least possible to implement the search feature of the classic start menu in a more efficient way? Just my opinion... -Alexandre

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[trinity-users] who is ezmlm?
by David Hare 16 Apr '13

16 Apr '13

> Hi! This is the ezmlm program. I'm managing the > trinity-users(a)lists.pearsoncomputing.net mailing list. > > I'm working for my owner, who can be reached > at trinity-users-owner(a)lists.pearsoncomputing.net. > > > Messages to you from the trinity-users mailing list seem to > have been bouncing. I've attached a copy of the first bounce > message I received. > > If this message bounces too, I will send you a probe. If the probe bounces, > I will remove your address from the trinity-users mailing list, > without further notice. ?

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Re: [trinity-users] Kick-Off Launcher
by dep 15 Apr '13

15 Apr '13

said Lisi Reisz: | On Monday 15 April 2013 14:18:05 Gerhard Zintel wrote: | > If you right klick the K-Meue there is an entry "Switch to | > Kickoff Menue Style" - there you are, you can switch between the | > two styles (Classical and Kickoff) easily. Even if I might not | > use it in future I've learned from this thread that it's there | > and I'm glad about it. | | Thanks, Gerhard. | | Even this right-click does not work on my Desktop! At least, it | does work and brings things up, but nothing about other menu | styles! Since this is only of academic interest - I have no desire | to change from the default TDE style, which I like - I shan't loose | any sleep over it. ;-) This is so on your machine even when you right click the KMenu icon in Kicker? I'd never seen it before, so I looked and there it was, though I dasn't click on the choice, lest I enter the tunnel of menu doom . . . -- dep The shortest distance between you and great fingerstyle guitar playing? The new instructional DVDs from Marjorie Thompson, available now at www.MarjorieThompson.com

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PCLinuxOS TDE non-official remaster Theme switch script
by Alexandre Couture 11 Apr '13

11 Apr '13

Hi everyone! I hope everybody had an happy Easter weekend! I wrote a little Zenity script to switch between the Classic and the Modern theme on my PCLinuxOS TDE non-official remaster. It will be available in the next version of my remaster, but is also works in the current version. I have posted here the pictures of the script. I will also host the next version of my remaster on MEGA instead of FileFactory, so I won't have to split the archive and it will be easier to download! You can download the script here: http://www.filefactory.com/file/6nkm9kcgtetl/theme_switch.zip If you have any comments, drop a line! -Alexandre

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Kmail deleting quoted text
by Greg Madden 10 Apr '13

10 Apr '13

I ma using Debian Wheezy + nightly builds I am unable to delete the quoted text part of a message I am replying to. I can delete other parts of my email. Anyone else seeing this behavior? TIA -- Peace, Greg

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Can Trinity run in linuxmint debian edition mate 64bit?
by dr lao 09 Apr '13

09 Apr '13

Despite having virtually all of trinity installed via synaptic using wheezy edition of nightly builds repo along with dependencies without problems, I cannot get tdm to run after the initial signin despite telling debian to use tdm not mdm. And tdm is not found in the choices available in the menu of options on signin. So can somebody please write a mint-meta-debian-tde analogous to the mint-meta-debian-kde and mint-meta-debian-mate which already exist ? tia!! dr_lao

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Re: [trinity-users] getting tid of trashcan on desktop
by dep 08 Apr '13

08 Apr '13

said Alexandre Couture: | > Subject: [trinity-users] getting tid of trashcan on desktop | > | > hi, good people . . . | > | > ever since kde 1.0 i have made a point of having *no* icons on my | > desktop. everything comes off of kicker or kmenu. | > | > today i did my usual daily update -- many things arrived -- and | > now i have an unremovable trashcan on my desktop. i do not object | > to having a trashcan. i have kept it as a nice little | > subdirectory off of ~/ for lo, these many years. this thing is | > not movable, though. i thought to find a desktop directory buried | > somewhere in ~/.trinity/ whence i could move it, but no joy. | > | > any idea how i can get rid of this thing? | > | > thanks! | > -- | > dep | | Hi! | Having the trashcan non-removable on the desktop seem to be a bug! | It works here for me, but if you can't delete it directly as you | could do with any icon: 1.Open the TDE Control Center | 2.Go in Desktop folder | 3. Click on the Behavior subfolder | 4.In the Device icons tab, you should be able to turn on/turn off | the Trash. | | Me too I prefer to have as few icons as possible on the desktop. I | find it more useful to have an analog clock widget and a calendar, | so I can keep track of my time :) | | Tell us if it works! | -Alexandre it did. i unclicked this in the rmb "configure desktop" setting -- it apparently didn't take. but now it did. many thanks! -- dep The shortest distance between you and great fingerstyle guitar playing? The new instructional DVDs from Marjorie Thompson, available now at www.MarjorieThompson.com

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getting tid of trashcan on desktop
by dep 08 Apr '13

08 Apr '13

hi, good people . . . ever since kde 1.0 i have made a point of having *no* icons on my desktop. everything comes off of kicker or kmenu. today i did my usual daily update -- many things arrived -- and now i have an unremovable trashcan on my desktop. i do not object to having a trashcan. i have kept it as a nice little subdirectory off of ~/ for lo, these many years. this thing is not movable, though. i thought to find a desktop directory buried somewhere in ~/.trinity/ whence i could move it, but no joy. any idea how i can get rid of this thing? thanks! -- dep The shortest distance between you and great fingerstyle guitar playing? The new instructional DVDs from Marjorie Thompson, available now at www.MarjorieThompson.com

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