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Fragment analysis software for linux

fragment analysis microsatellites AFLP linux software

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4 replies to this topic

#1 mboss

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Posted 24 June 2013 - 09:25 AM

Hi

I haven't been able to find a program that reads .fsa files and runs natively under linux. Currently I'm using PeakScanner in Virtualbox, which isn't ideal. I would appreciate if someone could point me to an appropriate program, preferably a free one.

Thanks.

#2 hobglobin

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Posted 24 June 2013 - 12:51 PM

not sure what you want to analyse (don't know peakscanner), but software based on java should do the job?
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#3 bob1

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Posted 24 June 2013 - 02:09 PM

How about Traceviewer (I haven't used it but it is win, linux and mac supported).

#4 mboss

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Posted 24 June 2013 - 02:14 PM

What I need is to score microsatellite (and AFLP) markers (i.e. I need to look at a .fsa chromatogram to check out the quality of the peaks and assign fragment lengths).

I haven't been able to find anything in java or in R. Traceviewer is for DNA sequences, not fragments.

#5 bob1

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Posted 24 June 2013 - 07:26 PM

I found this for R: http://people.oregon..._manual_v03.pdf (PDF)

Also: http://sourceforge.n...ts/genographer/





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