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Old 01-29-2009, 06:39 AM   #1
dlm
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Default User friendly ChIP-Seq software

Hello,
Does anyone know if any of the softwares for ChIP-Seq are suitable for use by non-bioinformaticists. ie. don't require command lines and have a friendly interface.
thanks v. much
DLM
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Old 01-29-2009, 11:06 AM   #2
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I don't think anyone's spending time setting up software interfaces for chip-seq applications yet... the underlying software is changing too quickly and it's not yet worth the investment. Personally, I'm just finishing my 4th major rewrite of the package I produce.

Somehow, I'm not sure what you're inferring, though - you shouldn't need to be a bioinformatician to follow the instructions in the manual to run a Chip-Seq package. Command lines really aren't that scary, and there is PLENTY of help available to get you started if you ask for it.

If running software from the command line is still too intimidating, and you want a bioinformatician to handle this part of the process for you, though, you can always contract out that part. (Heck, I'll do it in my spare time for you, if you leave me a tip. (-; )

Anthony
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Old 01-29-2009, 11:08 AM   #3
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Most user friendly is cisgenome chip seq browser
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Old 01-29-2009, 11:10 AM   #4
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I stand corrected, someone has put a user interface on chip-seq.
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Old 01-29-2009, 11:26 AM   #5
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Quote:
Originally Posted by apfejes View Post
If running software from the command line is still too intimidating, and you want a bioinformatician to handle this part of the process for you, though, you can always contract out that part. (Heck, I'll do it in my spare time for you, if you leave me a tip. (-; )

Anthony
Nice try Anthony ;-)
Moving towards rentacoder.com .. is a good idea though, game for developing it?
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Old 01-29-2009, 11:30 AM   #6
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Interesting - I'll have to look more carefully at it. Is there a demand for bioinformatics software coding?

Heh.. I might have to learn to write interfaces again...
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Old 01-29-2009, 11:34 AM   #7
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thanks guys
Command lines are still intimidating for a biologist! i was trying to spare our bioinformatician another sequencing project dumped on her but i appreciate the reasons and i'll have another crack!
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Old 01-29-2009, 11:41 AM   #8
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No worries.

I think most of the people who develop this software are aware that there are people running it who don't have a lot of computer experience and are willing to help out with questions. If you end up running FindPeaks, I'm always happy to do what I can to make the process as painless as possible.

The more people there are using the software, the more I learn about what works and what doesn't. (And the more incentive I have for writing a better manual, too!)

Good luck with your experiment, regardless of which package you choose!

Anthony
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Old 01-30-2009, 01:48 AM   #9
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I'm starting to use Galaxy as a front-end to my analyses now.

It's great for two main reasons:
1. you don't have to waste time writing interfaces
2. you can string multiple programs together in a 'workflow' by just using a browser
3. it's ridiculously easy to add in your own apps.

OK, that's three (and there are other compelling reasons), but I like it lots. Essentially, I want to move the donkey work onto Galaxy so the biologists can do the basics and I can spend time doing the 'interesting' stuff.
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Old 01-30-2009, 03:14 AM   #10
dlm
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Anthony,
thanks on your offer. i may get back to you if i struggle.
p.s. By the way your blogs are most informative
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Old 01-30-2009, 10:02 AM   #11
apfejes
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Hi Chris, thanks for the pointer to Galaxy. I hadn't seen it before, but it's pretty neat. I probably won't use it myself, as most of those things can be done very quickly with simple scripts, or going directly to the database, but it's obviously an excellent resource for people just getting started in the field.

dlm: glad you're enjoying the blog - it's a pleasure to write it! (=
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Old 04-13-2009, 06:27 AM   #12
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Quote:
Originally Posted by chris View Post
I'm starting to use Galaxy as a front-end to my analyses now.

It's great for two main reasons:
1. you don't have to waste time writing interfaces
2. you can string multiple programs together in a 'workflow' by just using a browser
3. it's ridiculously easy to add in your own apps.

OK, that's three (and there are other compelling reasons), but I like it lots. Essentially, I want to move the donkey work onto Galaxy so the biologists can do the basics and I can spend time doing the 'interesting' stuff.
Good to know galaxy is so nice!
I also start to use galaxy. I am wondering if there are somebody using a locally installed UCSC for galaxy instead of the official site of UCSC? for me i will use arabidopsis genome which is not offered by default in UCSC.
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