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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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