Getting Bowtie to work

[jamminbeh]

I installed bowtie from the sourceforge website, I unzipped it in a unix shell in windows, and when I try typing "make" inside of the newly made folder, there is an error saying it expects 2 more arguments. I've tried sound dis2unix for all files and I've tried it without it. Thank you for your help.

[jamminbeh]

the error message is:

make: *** No targets specified and no makefile found. Stop.

[jamminbeh]

I'm using Win32 version 0.10.0.2. After unzipping I typed:

./bowtie.exe e_coli reads/e_coli_1000.fq

and the results are:

x11drv: Can't open display:
Please ensure that your X server is running and that $DISPLAY is set correctly.

How can I fix this?

[joa_ds]

are you trying to use a bowtie.exe on a linux system?

You are probaly using the iTunes bowtie on a linux system.

Did you get bowtie from http://bowtie-bio.sourceforge.net/index.shtml?

[jamminbeh]

Yes, I downloaded it from that website, and i'm using a unix shell in windows.

[joa_ds]

Well, linux has no .exe extensions. So trying to use that .exe bowtie will never work. You should get a linux version to run in your linux shell.

[Ka123$]

sortFiles problem

Hi , Can anyone help me with this problem please.
I have bowtie aligned seq and trying to convert it into wigfiles using the findpeak.
so I performed a SeparateReads and saved it in a folder as per the manual.When I tried using the SortReads on the gz file in the separatereads...I get an error saying : java : no match....
I do have the java jre path set and it worked for the separatereads..
Is it that I need to unzip the gz file and perform it?
Any help? THanks

[Ka123$]

Sort files

Ohk I got to work the sort files on my separate files to run! But it went out of memory!!!
Exception in thread "main" java.lang.OutOfMemoryError: GC overhead limit exceeded
Any suggestion on how to fix this problem?

[Ka123$]

If I used the SeparateReads from findpeaks directly on GERALD.export files ,specifying the -aligner eland, I get an error message: Any help?
Version: Initializing class SeparateReads $Revision: 1082 $
Version: Initializing class Log_Buffer $Revision: 1145 $
Version: Initializing class Generic_AlignRead_Iterator $Revision: 1318 $
Version: Initializing class ElandIterator $Revision: 841 $
Error: Error processing mistmatch type 7 on line 1of Eland file

[ikrier]

Did you try using eland_extended?
__ you probably solved this, so I wish I could remove my post