RNA-seq mapping on Windows

Question

[K.Nijbroek]

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.

[bull.fabian]

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.

[Bharat Iyengar]

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.

[poisonAlien]

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

Answer 1

[Bharat Iyengar]

You can run tophat on cygwin

[K.Nijbroek]

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?

[Bharat Iyengar]

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.

[K.Nijbroek]

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)....

[carol091188]

Hey, how can I do that? can you give me some tips about it?

Thank you