CONTRA for CNV analysis

Dec 14, 2012 at 9:42 AM

Hi,

I'm not a bioinformatician, and I found great to be able to work under windows on BAM files thanks to the samtools.exe which you had provided here.

As part of my current research project, I wish I could analyze CNVs from targeted resequencing data. I found several tools, but none that I could easily use given my lack of bioinfomratic skills. For instance, I found the CONTRA software package developed by Li et al (http://contra-cnv.sourceforge.net/). Yet, it works with Linux. I wondered whether it would be feasible to adapt it to dos windows. I would be very helpful for biologists.

Regards,

Sébastien

Coordinator
Dec 14, 2012 at 2:30 PM

Hi, Sébastien

Neither am I a bioinformatician, so we don't need worry about the titles.

I had a look of CONTRA, it doesn't look like a 'concrete' program/software, more on the side of a bundle of scripts calling other 'real' programs. In some way this can be called a 'pipeline' for CNV analysis.

Of the components required:

  • Python 2.6+
Most of the scripts for CONTRA are written in Python. It requires version 2.6 in order to use the multiprocessing module.

We have IronPython on Windows, http://ironpython.net/

  • R (now support all versions of R)

R does run on Windows

  • BEDTools (Included in CONTRA package. See Installation Guide)

BEDTools in fact use Bamtools, I'm in the middle to port Bamtools, then will do the BEDTools port.

  • SAMtools

We have it here.

  • [Optional] DNACopy (R-library that will be used for predicting large CNV)

Hope this R-library will just run fine.

Seems to me the road blocker is really BEDTools in the whole chain.

Best,

dong

Dec 14, 2012 at 3:00 PM

Hi Dong,

Thanks for your reply. I was not aware of ironpython. I guess that another interesting tool for CNV was written exclusively in Python. I will see what I can do with other tool (I don't remember if it was CoNIFER or another one) and how far I can go with CONTRA depending on the step at which BED Tools is required.

Best regards,

Sébastien

Coordinator
Jan 17, 2013 at 1:05 PM

Hi, Sébastien

How is things going? Which package did you choose? Does that work alright?

Best,

dong

Jan 18, 2013 at 4:43 PM
Hi Dong,

Actually, I had many difficulties with ironpython. I spend many time trying to use it properly.
Thus, I decided to try a demo proposed by NextGENe, which works with windows. It's not a long-term option, but, at least, I could analyze my data.

Best wishes,

Sébastien


From: [email removed]
To: [email removed]
Date: Thu, 17 Jan 2013 05:05:40 -0800
Subject: Re: CONTRA for CNV analysis [bow:406750]

From: xied75
Hi, Sébastien
How is things going? Which package did you choose? Does that work alright?
Best,
dong
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