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  • wuhoucdc
    replied
    Thanks ECO for your kind suggestions.

    Wuhoucdc

    Leave a comment:


  • ECO
    replied
    Originally posted by wuhoucdc View Post
    Hi all,

    Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

    Wuhoucdc
    You are more than welcome to start annotating the software packages in our wiki: http://wiki.seqanswers.com. I believe Dan is working on a set of instructions for new wiki users.

    Thanks!

    Leave a comment:


  • wuhoucdc
    replied
    Hi all,

    Who have the time to summarize the programs that can be used call SV such as large rearrangement, deletion, amplication among NGS? Thanks.

    Wuhoucdc

    Leave a comment:


  • dan
    replied
    Originally posted by Y.Y. LEUNG View Post
    Hi All,

    I am a new user of NGS softwares. Thanks a lot for providing such a list. Are there any updates on the information provided?

    with so many tools (e.g. in the ALign/assemble field), do anyone has any idea on which tool are the best for use (in terms of ease of usage and computation time required)?
    I know the feeling!

    I'm going to start a 'standard operating procedures' (SOP) section on the wiki to document case studies based on various requirements.

    Basically the answer to your question depends on what data you have, what you are trying to do with your data, and what OS you are familiar with. If you can supply those details, I'm sure there will be several suggestions of how to proceed.

    Leave a comment:


  • Y.Y. LEUNG
    replied
    What is the best Align/Assemble tool?

    Hi All,

    I am a new user of NGS softwares. Thanks a lot for providing such a list. Are there any updates on the information provided?

    with so many tools (e.g. in the ALign/assemble field), do anyone has any idea on which tool are the best for use (in terms of ease of usage and computation time required)?

    Thanks a lot.

    Fanny Leung

    Leave a comment:


  • dan
    replied
    Originally posted by dan View Post
    I still haven't got the query interface working to get proper reports on contributions.
    Here is is finally!

    The result is pretty awesome! Thanks everyone for taking part!

    (I'll break this down to remove 'robot' edits, which is the reason why I currently have so many)

    Code:
    SELECT
      user_name, user_editcount 
    FROM 
      user 
    ORDER BY 
      user_editcount DESC 
    ;
    
    user_name	user_editcount
    Dan		478
    Krobison 	229
    Andreas.sjodin 	209
    ECO		56
    Cariaso 	12
    Taoliu		5
    Maubp		5
    Apfejes 	4
    Nilshomer 	4
    Simonandrews 	4
    Weese		4
    Wjeck		3
    Yxi		3
    Ohomann 	3
    BaCh		3
    Dfornika 	3
    HAA		3
    Jkbonfield 	2
    Ben Langmead 	2
    Kevleb		2
    Joa ds		2
    Dawe		2
    Balajis 	1
    Lparsons 	1
    Jonathan 	1
    AlwaysSNP 	1
    Mmartin 	1
    Lh3		1

    Leave a comment:


  • ECO
    replied
    Originally posted by dan View Post

    P.S. Perhaps ECO should archive/sticky this thread, create a forum for the wiki and somehow (sticky thread?) let people know to start using the wiki?
    I've been considering losing this thread for a while, mainly because any replies in this thread end up emailing about 50% of the members who have either subscribed or posted in the thread (Hi everyone! ).

    The second improvement would be to link all these packages to their respective wiki pages.

    As a side note, I don't want anyone to get wedded to the new domain seqwiki.com, as the seamless cross-site authentication with the forum accounts does not work. Seqwiki.com is fine for viewing, but wiki.seqanswers.com will be the only one that is editable for a while. (They share the same database). Let's keep this discussion in another thread, perhaps in that "Wiki Development" forum I keep forgetting to set up.

    Originally posted by ohomann View Post
    Hi Dan,

    Thanks, I actually found the wiki and added MochiView just after posting to this thread. FWIW, the upload image option doesn't seem to work (it tells me that I don't have a proper extension on my file).

    Thanks for the great resource!
    Hmm...perhaps Dan could fix this.

    Leave a comment:


  • ohomann
    replied
    Originally posted by dan View Post
    Hey Oliver,
    Please have a go at adding MochiView to the wiki, and let us know how you got on (any good / bad features, etc.).
    Hi Dan,

    Thanks, I actually found the wiki and added MochiView just after posting to this thread. FWIW, the upload image option doesn't seem to work (it tells me that I don't have a proper extension on my file).

    Thanks for the great resource!

    Leave a comment:


  • dan
    replied
    Hey Oliver,

    I've been working developing the 'wiki arm' of the SEQempire (called SEQwiki) so that it can be used as a browsable / query-able archive of "Software packages for next gen sequence analysis" [1]. The content was seeded from a table on the NBIC wiki [2], which was originally seeded from this list!

    It's still work in progress, but the best 'first impression' is probably here:




    (Lots of packages still need data adding.)

    Since setting it up there have been quite a few packages added, mostly by KRobinson but also many others [3]. Please have a go at adding MochiView to the wiki, and let us know how you got on (any good / bad features, etc.).

    Cheers,
    Dan.

    [1] http://seqwiki.com
    [2] http://wiki.nbic.nl/index.php/High_t...ncing#Software
    [3] http://seqanswers.com/w/index.php?ti...s=30&limit=500 - I still haven't got the query interface working to get proper reports on contributions.


    P.S. Perhaps ECO should archive/sticky this thread, create a forum for the wiki and somehow (sticky thread?) let people know to start using the wiki?

    Leave a comment:


  • ohomann
    replied
    Hello everyone,

    I was wondering if you would mind adding MochiView, my hybrid genome browser and motif visualization/analysis software, to this list.

    Here is a link to the section of the MochiView website with three quick demo videos.

    MochiView is particularly useful to anyone interested in identifying/analyzing/managing motifs (multiple motif libraries are available on the MochiView website for import into the software). In addition, members of various labs around UCSF are using the software to visualize/analyze Chip-Chip, Chip-Seq, and RNA-Seq data.

    Here are a few more details for those interested:
    • MochiView is desktop Java software with an integrated database
    • MochiView has a rich interface for configuring/saving plot layouts
    • The browser has smooth panning/zooming and a very useful data browsing function
    • MochiView contains a large number of motif utilities, including motif comparison, motif position distribution, motif ROC plots, several motif scoring functions, ability to rapidly export motif scoring of location sets or promoters to spreadsheet, etc.
    • MochiView also contains some Location/Data Set manipulation utilities (e.g. set operations and filters)
    • The website contains a tutorial for download that can familiarize you with many of the basic features
    • MochiView will write and publish your paper for you. OK, that feature isn't quite ready yet


    One thing MochiView does NOT do is "peak-calling" for Chip-Chip or Chip-Seq. MochiView leaves this to the many existing solutions and is more appropriate for downstream visualization and analysis.

    Thanks for your time,
    Oliver Homann
    Johnson Laboratory
    UCSF

    Leave a comment:


  • sci_guy
    replied
    Cheers

    Originally posted by wuhoucdc View Post
    Thanks Sci_guy pasted such a great resource!
    Also big ups to ECO, Dan, et al. for the Wiki. I've been on the back foot lately in maintaining this list; too busy in the lab. An abstract deadline for the AACR Cancer Epigenetics conference next year to meet

    Leave a comment:


  • wuhoucdc
    replied
    Thanks Sci_guy pasted such a great resource!

    Leave a comment:


  • Xi Wang
    replied
    Hi all,

    Have you noticed a review on ChIP-seq and RNA-seq computational studies? It mentioned and summarized some available tools on ChIP-seq and RNA-seq data processing.



    Review
    Nature Methods 6, S22 - S32 (2009)
    doi:10.1038/nmeth.1371
    Computation for ChIP-seq and RNA-seq studies
    Shirley Pepke1, Barbara Wold2 & Ali Mortazavi2


    Best wishes,
    Xi

    Leave a comment:


  • ewilbanks
    replied
    Try TopHat http://tophat.cbcb.umd.edu/

    It uses Bowtie to map reads and analyzes the mapping results to identify splice junctions between exons.

    Leave a comment:


  • apfejes
    replied
    We use a database of all predicted/potential exon/exon junctions in addition to the genome, and then use maq/bwa - it seems to do very well.
    Last edited by apfejes; 10-27-2009, 07:12 AM. Reason: too sleepy to get it right the first time.

    Leave a comment:

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