Hi,
Is there a good RNA-seq mapping tool that is also able to identify splice sites, which can be run on Windows 7?
Thanks.
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K.Nijbroek •
You can run tophat on cygwin
Thanks! Thats exactly what I hoped for. I'm now installing Cygwin with ALL packages. Could you perhaps give me some details of the steps to implement tophat on cygwin?
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K.Nijbroek •
You can either compile tophat or use the binaries. You don't need all packages. Just use the ones that you really require, else it will take a long time to download and install. You would also need samtools and bowtie to run tophat.
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Bharat Iyengar
Installed samtools, bowtie and boost (as manual said). Now make tophat2 running into the error that aio.h can not be found (which is not included in cygwin)....
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K.Nijbroek •
Hey, how can I do that? can you give me some tips about it?
Thank you
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I don't know a single tool that can not be compiled under windows 7. So pick one and try it out. Besides that, OS dependence should not be your favorite concern when choosing a mapping tool.
Sometimes compiling with makefiles can be small problem. Also windows would require the C-compiler.
But I agree with you though I have not done it myself. This post may be worthwile to look at.
Check this: Bioinformatics on windows
I think you can get .exe's for samtools, tabix, bwa and for some more. -_-
Not sure about RNA-seq mapping tools