findpeaks s/w
does findpeaks only accept eland files? what other files i can run using findpeaks?
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ace files from MAQ or SOAP alignment viewable in EagleView
Anyone tried that? Converting the MAQ or SHrimp alignment to .ace file format, which can be used in the EagleView tool from Marth Lab?
I was looking for a good way to convert alignments to .ace file format
sm
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Originally posted by bioinfosm View PostThanks apfejes
I know of the FindPeaks tool ... the others you mention are available somewhere to download and try?
I am looking to use a few of the short read tools available to see how they perform on the solexa data,. and what tweaks i can learn... but that requires being able to go from their output to something more friendly
next, the visualizations are just a good way to be able to depict data, in case it is feasible
Sorry - they're not publicly available yet, but I'm always looking for beta testers/collaborators. Send me a PM, if you're interested.
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Originally posted by ECO View PostI've read in a couple of places that someone has written an ELAND-->GBrowse script that will let you view the assembly in Gbrowse...but I can't find any actual projects.
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Originally posted by todd View PostThanks ECO,
Geospiza is a software company in Seattle specializing in automation systems for genetic analysis. We have products (FinchLab and iFinch) to handle both LIMS and analysis needs for Next Gen sequencing. These products are being delivered in novel cost effective ways so that groups do not have build data centers for their new machines.
Many folks know of us from FinchTV. To learn more you can visit our web site . You can also check out our blog FinchTalk, where we give short demos and discuss the issues we see with next generation sequencing.
Please visit, we'd like to hear what you are doing and see if we can help.
Cheers,
Todd
Geospiza, Inc.
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I've read in a couple of places that someone has written an ELAND-->GBrowse script that will let you view the assembly in Gbrowse...but I can't find any actual projects.
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Who is Geospiza?
Originally posted by ECO View PostI have, but I haven't heard much about their service. I would invite them to come and introduce the community to the service.
Geospiza is a software company in Seattle specializing in automation systems for genetic analysis. We have products (FinchLab and iFinch) to handle both LIMS and analysis needs for Next Gen sequencing. These products are being delivered in novel cost effective ways so that groups do not have build data centers for their new machines.
Many folks know of us from FinchTV. To learn more you can visit our web site . You can also check out our blog FinchTalk, where we give short demos and discuss the issues we see with next generation sequencing.
Please visit, we'd like to hear what you are doing and see if we can help.
Cheers,
Todd
Geospiza, Inc.
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Originally posted by apfejes View PostTo answer the part on visualization, I have several tools that create files that are viewable on the UCSC genome browser. or generate a text file showing the aligned reads against the canonical sequence. I now even have a tool for generating post script files of peaks (for Chip-Seq experiments) along entire chromosomes.
The question is really what you're looking for. It's easy to visualize this data, but very hard to create new views that give new insight.
I know of the FindPeaks tool ... the others you mention are available somewhere to download and try?
I am looking to use a few of the short read tools available to see how they perform on the solexa data,. and what tweaks i can learn... but that requires being able to go from their output to something more friendly
next, the visualizations are just a good way to be able to depict data, in case it is feasible
Leave a comment:
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To answer the part on visualization, I have several tools that create files that are viewable on the UCSC genome browser. or generate a text file showing the aligned reads against the canonical sequence. I now even have a tool for generating post script files of peaks (for Chip-Seq experiments) along entire chromosomes.
The question is really what you're looking for. It's easy to visualize this data, but very hard to create new views that give new insight.
Leave a comment:
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parsing the output
How are people making use of outputs from various tools?
For instance
soap has this one line format with its way of representing variation
shrimp seems even more complicated with a fasta line format not even mentioning where the substitutions / indels are ... even if you look at the prettyplot
Any views on visualizing the data on global scale .. giving an indication of depth of sequencing at various regions on the reference, % variation... etc?
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GeoSpiza
Anyone heard of them? or their suite of tools for next gen data analysis, visualization and management?
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As we could imagine, this list of programs will grow very fast. And here are more:
Euler-SR (Euler-Short Reads Assembly, http://euler-assembler.ucsd.edu/portal/) by Mark J. Chaisson and Pavel A. Pevzner from UCSD. (published in Genome Research)
RMAP (A program for mapping Solexa reads, http://rulai.cshl.edu/rmap/) by Andrew D. Smith and Zhenyu Xuan at CSHL. (published in BMC Bioinformatics)
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I've found some time to update the table with Heng's and Anthony's extra info. Thanks guys.
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Thanks Anthony, updated the spelling change. I'll leave it to sci_guy to condense the content in his list.
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