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Old 07-28-2009, 04:00 AM   #161
BaCh
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Quote:
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Complex answer, how do we actually want to model the software? i.e. what tables, fields and values would you use to build a database of packages?
I try to look at that problem from the perspective of a user:
I have X1 reads of type T1, which assembler can do de-novo assembly with that type? Or mapping assembly and if yes, does it output differences to the reference sequence?
If I then throw in X2 reads of type T2, which assemblers can use both read types for a hybrid assembly strategy?
For that the programs should get tags which denote their capabilities like "denovo Solexa", "denovo 454", "mapping Solexa", "SNP calling", "hybrid assembly" etc.pp so that users can iteratively filter to what they need.

Other aspects would be harder to tag like, e.g., up to which data quantity a certain program should be used etc.pp and when another program would be appropriate.

Just some random thoughts,
B.
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Old 07-30-2009, 06:32 AM   #162
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Default GenomeQuest

Dear all,

Just a brief message to point you also to GenomeQuest's new beta offering in NGS sequence data management and analysis. (COMMERCIAL ALERT! Please note that I am self-promoting as I am the VP of Software for the company.) However, I think the offering is pretty exciting and may be valuable for researchers and bioinformaticists. For you to decide...

You can try it for free with no obligation: www.genomequest.com. It runs in your web browser.

Currently we support RNA-Seq, Variant calling, Rapid Annotation (metagenomics), and long read assembly, as well as high-throughput mapping. CHiP-Seq, micro RNA, other assembly tools, and much more will be rolled out shortly. All of the world's reference data is kept up to date inside the system so you get up-to-the-minute accuracy. And you can upload and use your own reference data if you prefer. Of course, there are APIs for bioinformaticists to extend and integrate the system, and we're about to release a huge update to the APIs that make it stronger still. Again, much much more to come in the coming weeks and months. I'll let it speak for itself.

Most importantly, we're looking for your detailed help to make it better. We have a linkedin group for feature requests at http://www.linkedin.com/groups?gid=2056733 and I'd welcome any comments you have directly via email, as well.

Thanks for letting me have the opportunity to announce the new product.

Best regards,
Richard
richard.resnick@genomequest.com
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Old 08-05-2009, 08:08 AM   #163
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Default Open source Vs Commercial

Hi Folks, I an new to NGS and am tasked to evaluate commercial and open source alternatives to analyse NGS data. Looking at the pretty comprehensive list in this post (which is very useful) I am not able to make out whether we really need to pay for a solution such as Genomatix or can we do away with just the free open source tools?

Please comment or share your thoughts in this regard.

I Appreciate your time and inputs.
Thanks,
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Old 08-05-2009, 08:14 AM   #164
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Hi hrajasim,

That's a very open ended question, depending very strongly on what type of analysis you'd like to do. As far as I'm aware, the cutting edge development for NGS is happening in open source, so you'll probably want to fill major parts of the pipeline with open source (Eg, aligners, format converters, ChIP-Seq analysis, assembly, etc)

However, any time you're contrasting open source versus a commercial product, you have to ask the right questions:

Is there a feature set that I absolutely need?

Will I require support for the software beyond the forums and available community?

Will I want to make modifications to the source code and customize it for the pipeline?

Without knowing what you plan to do with the software, it will be impossible for us to figure out which path is best for you.

Cheers!
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Old 08-05-2009, 02:44 PM   #165
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Further to the above, if you're a molecular biologist without coding skills it is far easier to stick to commercial integrated solutions however you may feel constrained by lack of features within the software if your application is anything other than vanilla.
If you embark upon the open source route you'll need skills in UNIX shell scripting/Perl/SQL. If you don't have them get a bioinformatician onboard. If you need to do 'counting' methods such as RNA-Seq, CHiP-Seq, Bis-Seq, etc then it is probably wise to consult a biostatistician.
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Old 08-06-2009, 01:08 AM   #166
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Exclamation

Thanks for your useful post.

I’m interested in ABySS and I installed it on my linux server.
However, I knew it does not use a reference genome, as it is a de novo assembler.
I think it should be moved from "Align/Assemble to a reference" category to "De novo Align/Assemble" category.

Cheers! ^^
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Old 08-06-2009, 03:57 PM   #167
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Quote:
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...I think it should be moved from "Align/Assemble to a reference" category to "De novo Align/Assemble" category.
Done. Thanks
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Old 08-10-2009, 01:03 AM   #168
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Great list!
I'd like to introduce some code I'm working on. I don't know if it deserves to go into the list, but it might be of some use for someone. Is not finished yet, but if someone is interested in trying it out or in working on it just let me know.
You can find it at biolib.
It's a library and a set of script targeted to NGS. There are modules to:
- clean sequences (sanger, 454, ilumina).
- parse caf, ace and bowtie map files.
- clean and filter contigs.
- look for snps and indels.
- filter snps.
- do statistics for: reads, contigs and snps.

Be aware that it's just a work in progress and its in constant flux. The code is available under the AGPL.
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Old 08-18-2009, 02:19 PM   #169
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Default Beta version of the SEQwiki software database up and running...

Check it out...

http://seqanswers.com/wiki/SEQanswers
http://seqanswers.com/wiki/Software


Dan.
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Old 08-18-2009, 02:27 PM   #170
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Hey, that's awesome - Great Job!
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Old 08-18-2009, 11:45 PM   #171
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Hi all,

Thanks for the helpful list. Based on reading the post I've tried out Bowtie to align reads from a ChIP-seq experiment run on Illumina GA-II (the facility gave me non-aligned fastq). Worked great!

I want to put the output into cisGenome or FindPeaks (or both). Can anyone advise me how to get it into the right format? Does FindPeaks convert any of the output options in Bowtie?

Thanks
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Old 08-19-2009, 07:58 AM   #172
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Hi Dinny,

Findpeaks can use bowtie's reads - but it depends if you want to use PET or SET tags. if you're using PET, you'll need to convert your reads into BED format, which is the only way that you can retain the pairing information. If you're using SET, you should be able to bet Bowtie to produce a .map file (if I recall correctly), which can then be processed natively by FindPeaks.

If you need help with findPeaks, you can always send an email to the mailing list - I tend to reply more quickly to those inquiries than those on SeqAnswers.

Cheers,
Anthony
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Old 08-19-2009, 08:44 AM   #173
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I don't think that CisGenome has support for bowtie output yet. Best bet would be to find scripts to convert to .bed or .aln
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Old 08-20-2009, 03:40 AM   #174
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Thanks very much Anthony and ewilbanks.
I looked closer at Bowtie conversion tools and I can create a .map file from the alignment (I'm working with single-end reads), but I have to get Maq working to do it. I'll give it a go, and compare Maq alignment times while I'm at it ;-)
Cheers,
Dinny
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Old 08-20-2009, 06:19 AM   #175
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Hi Dinny,

I think there is also a way to get Bowtie to produce it's own alignment in .map format, if I recall correctly.

Anyhow, if you're working with SET, you can also convert the bowtie reads directly to .bed: https://sourceforge.net/apps/mediawi...e=ConvertToBed
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Old 08-20-2009, 09:23 AM   #176
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what is the definition of the header line in SOLiD csfasta file, eg
1_88_1830_R3 -- What is 88, 1830 stands for ? Thanks
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Old 08-20-2009, 12:55 PM   #177
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Quote:
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what is the definition of the header line in SOLiD csfasta file, eg
1_88_1830_R3 -- What is 88, 1830 stands for ? Thanks
See http://seqanswers.com/forums/showthread.php?p=7572.
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Old 08-21-2009, 03:53 AM   #178
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Hi Anthony,
Thanks again for the advice. Taking the reads directly into .bed would be better. The .map converter in Bowtie needs a library file created in Maq, so it would be easier to limit the number of applications the data goes through...less opportunity to completely jumble it.
Couldn't see a way to align straight to .map, but I'll look again.
Dinny
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Old 09-24-2009, 06:51 AM   #179
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Default Solexa findpeaks

Using Findpeaks sort reads on bowtie mapped alignment is taking up too much memory......!!!!! So I am trying using the GERALD maps reads directly from solexa to convert to wig files...I believe the solexa GERALD mapped alignments are ELAND format?
So the aligner type will be -aligner eland, to perform separateReads.jar?
Any suggestions?
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Old 09-24-2009, 08:43 AM   #180
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Hi Ka123,

There are other ways to do the sort - including several methods you could try from the linux command line. However, I'm really not sure why it's taking so memory. Could you give me a few ideas as to what your work flow is?

In the meantime, documentation and an example command for SeparateReads can be found here:

https://sourceforge.net/apps/mediawi...=SeparateReads
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