Is there a good RNA-seq mapping tool that is also able to identify splice sites, which can be run on Windows 7?
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
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?
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.
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)....
Hey, how can I do that? can you give me some tips about it?
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