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.
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the error message is:
make: *** No targets specified and no makefile found. Stop. -
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?Comment
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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?Comment
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Yes, I downloaded it from that website, and i'm using a unix shell in windows.Comment
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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.Comment
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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? THanksComment
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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?Comment
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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 fileComment
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Did you try using eland_extended?
__ you probably solved this, so I wish I could remove my post
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