Thanks Sci_guy pasted such a great resource!
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Cheers
Originally posted by wuhoucdc View PostThanks Sci_guy pasted such a great resource!
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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
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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?
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Originally posted by dan View PostHey Oliver,
Please have a go at adding MochiView to the wiki, and let us know how you got on (any good / bad features, etc.).
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!
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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?).
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 PostHi 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!
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Originally posted by dan View PostI still haven't got the query interface working to get proper reports on contributions.
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
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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
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Originally posted by Y.Y. LEUNG View PostHi 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'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.
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Originally posted by wuhoucdc View PostHi 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
Thanks!
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Originally posted by Y.Y. LEUNG View PostSeems that most of the softwares are available in Linux environment.
Are there any softwares recommended for use in Windows for RNA-seq or targeted sequencing projects? the data are obtained from Solexa, 454 and SoLID.
Thanks for your help.
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Depends what you're trying to do - I've used Vancouver Short Read Analysis Package/FindPeaks (my own software) for RNA-Seq (alternative exon expression) and had good luck - I don't use it in windows, myself, but java is cross-platform and I know people have successfully used in that environment.The more you know, the more you know you don't know. —Aristotle
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