Bowtie for Windows 7

[xuguorong]

I tried to install bowtie on my windows 7 32bit and 64bit, and I found it cannot align large size data set. When I used the indexes file of H. sapiens (2.7GB), bowtie told me that cannot load the indexes files. Even I run only one chromosome fasta file, bowtie still cannot always run successfully.
Anybody knew this solution?

Thanks

[RDW]

I don't know if this is your issue, but if you got the Windows binary from Sourceforge it's 32-bit only, even if you run it under 64-bit Windows. To get a 64-bit binary you'd have to build from source with a compiler that supports 64-bit output. Installing 64-bit Linux might be easier, especially when you need to use other tools in future.

[xuguorong]

Hi RDW,

I downloaded the 32bit binary bowtie from the sourceforge and tried to run on my 32bit Win 7 machine. The fasta/fastq file cannot exceed 10K reads, otherwise bowtie always exit automatically and the output .sam file is also not completed.
I tried 3 machines and still got the same problem but Linux and Mac version work well.
Any ideas about this problem?

[RDW]

Sorry, perhaps I didn't put that very clearly. I was guessing that 32-bit is the problem - you need a 64-bit version to process larger files. For the Linux and Mac versions, the Sourceforge site has 64-bit bowtie binaries you can run on the 64-bit versions of these operating systems. Unfortunately, the Sourceforge site only has a 32-bit bowtie binary for Windows available. Although this will run on either version of Windows, it will always run in 32-bit mode, even on 64-bit Windows.

My guess is that, if you must use Windows, you need to run a 64-bit bowtie for Windows binary on a 64-bit version of Windows 7. Since you can't download a 64-bit bowtie for Windows binary from Sourceforge, you'd have to compile one yourself from the source code, using an appropriate compiler (make sure it supports generating 64-bit executables, and that any necessary compiler flags have been set). I haven't tried this, and don't know how difficult it would be - I would suggest using Linux or Mac instead if you don't already have experience in compiling for 64-bit Windows.

[xuguorong]

Hi RDW,

Thank you for your reply!
Yes, I tried 32bit binary and it cannot process large files. I also tried to compile 64 bit from source code but failed. So I have to switch to Linux or Mac OS to process large file.

I really appreciate your help again!