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Old 03-22-2009, 02:55 PM   #121
alig
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Consed is very similar to gap4 and now assembles illumina short reads.

I have been happy with the assembly to a reference sequence & the contig viewer & searching for highly discrepant regions.

hope this is of help

alig
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Old 03-22-2009, 11:57 PM   #122
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Default CNV-seq

a package to detect DNA copy number variation using shotgun sequencing.
http://tiger.dbs.nus.edu.sg/cnv-seq/
http://www.biomedcentral.com/1471-2105/10/80
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Old 03-26-2009, 06:44 PM   #123
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MapView: a short reads alignment viewer with genetic variation analysis, visualization of short reads alignment on desktop computer

http://evolution.sysu.edu.cn/mapview/
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Old 03-31-2009, 01:46 PM   #124
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Quote:
Originally Posted by kopi-o View Post
I didn't see MACS and PeakSeq among the ChIP-seq peak callers. Those should be added.
Seconded. MACS is a useful tool.
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Old 04-01-2009, 12:52 AM   #125
xuer
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Quote:
Originally Posted by RudyS View Post
thanks swbarnes2

i think i will post a query on the UCSC listserver
[email protected]
and see if someone like Jim Kent is thinking about some utility that could facilitate reference assembly on a local Genome Browser ... he's the guy i think who initiated BLAT and isPCR on their site

http://genome.ucsc.edu/

the browser can be installed locally and used with any genome ... but without taking into account quality values from the reads its hard to imagine not getting just a mess doing a BLAT-like alignment ... i think

RudyS
Is there anybody have the experience to install UCSC locally with other genome database like arabidopsis? I hope I can find a detailed procedure to set it locally.
Thanks!
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Old 04-01-2009, 04:42 AM   #126
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xuer
the browser is well documented ... suggest you write to the nice folks on the listserver there

[email protected]

Rudy
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Old 04-02-2009, 06:13 AM   #127
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Default Meeting in Berlin this month

Xuer, you might also access TAIR scientists who will be attending the International Biocuration Conference in Berlin later this month.
http://projects.eml.org/sdbv/events/.../schedule.html
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Old 04-13-2009, 04:50 AM   #128
xuer
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RudyS,Thank you for the reply.for me the Installation if UCSC is finished, next i need to set the arabidopsis assembly. hopefully it goes well.

Joann, Thank you for the information.The topics are interesting , i hope i could be there.
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Old 04-21-2009, 11:40 AM   #129
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Default How about Genomatix?

Hate to be so blatantly commercial, but in the "not for free" category, you should add Genomatix. No sales pitch here...but check out the vendor forum! Complete analysis capabilities for all current platforms...thanks.
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Old 04-22-2009, 05:45 PM   #130
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Release V2.03.12 of Novoalign is out. This release improves performance especially for longer reads and is a 4-5 times faster on 45bp reads against Human. Longer reads have improved even more. Performance improvement is more pronounced when allowing more mismatches (higher thresholds).

It also seems our web site has been blocked in China so if any one in China wants a copy of novoalign please email me at colin at novocraft dot com. I'll create a mailing list and keep you informed of any updates etc.
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Old 04-23-2009, 07:45 AM   #131
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I think it will be a good idea to include RNA-SEQ tools in the huge table. The one tool I know for that = erange
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Old 05-08-2009, 04:35 PM   #132
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Any more ChIP-seq analysis tools that we should add here?

Also, does anyone know if the program from the Poisson mixture method paper is publicly available?:
http://www.biomedcentral.com/1471-2164/9/S2/S23

Or if anything has been published about the ChIP-seq Analysis server?
http://ccg.vital-it.ch/chipseq/
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Old 05-09-2009, 02:11 AM   #133
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Quote:
Originally Posted by ewilbanks View Post
Any more ChIP-seq analysis tools that we should add here?
The Bioconductor 'chipseq' package / programs should be added for sure! See also the other thread on this topic:

http://seqanswers.com/forums/showthread.php?t=742
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Old 05-14-2009, 10:47 AM   #134
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Default RNA-seq tools?

Quote:
Originally Posted by bioinfosm View Post
I think it will be a good idea to include RNA-SEQ tools in the huge table. The one tool I know for that = erange
I'd like to second the call for including RNA-seq tools, e.g. ERANGE, TOPHAT, G-Mo.R-se... any others??
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Old 05-14-2009, 11:00 AM   #135
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Quote:
Originally Posted by mbjohnson View Post
I'd like to second the call for including RNA-seq tools, e.g. ERANGE, TOPHAT, G-Mo.R-se... any others??
Also RSAT
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Old 05-14-2009, 11:00 AM   #136
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I have a fairly complete set of RNA-Seq tools in the Vancouver Short Read Analysis Package, although they've never been published.
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Old 06-07-2009, 06:37 PM   #137
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spam? The hidden link is pretty sneaky.
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Old 06-07-2009, 06:45 PM   #138
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Quote:
Originally Posted by apfejes View Post
spam? The hidden link is pretty sneaky.
Yup, I got 'em in moments, but I'm considering adding moderation of posts to this thread so everyone doesn't get emailed when that happens. :/
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Old 06-07-2009, 06:51 PM   #139
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Thanks ECO,

It's so hard to stay one step ahead of the spammers. I probably should have refreshed before replying. Sorry to those who are getting excessive emails. :/

Anthony
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Old 06-15-2009, 01:13 AM   #140
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Hi thread followers,

I've spent most of the last year in the wet lab implementing a new epigenomics method for SOLiD and Illumina so I've had no time to update the table at the start of this thread. I'm moving onto the 'dry' phase now and are hunting around for software to assist in my analysis. Anyway, I took this opportunity to update the table. Apologies to those who have PMed me over the last long while asking for their software to be added.

I hope to keep this table a little better maintained, but the amount of software out there is exploding (just like the amount of data and potential applications of 2nd Gen Seq). In light of this I cannot promise the table will be comprehensive for that much longer.

Cheers,
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