Tweet
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.
-
-
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
-
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
-
Yes, I downloaded it from that website, and i'm using a unix shell in windows.Comment
-
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
-
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
-
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
-
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
-
Did you try using eland_extended?
__ you probably solved this, so I wish I could remove my post
Comment
-
Proteomics platforms are evolving rapidly, with advances in mass spectrometry and affinity-based approaches expanding what researchers can detect and at what scale. As the field moves toward deeper proteome coverage and clinical applications, scientists face an increasingly complex landscape of tools. This article will explore how researchers are navigating these choices to find the right platform for their work.
The systematic characterization of the human proteome has...07-20-2026, 11:48 AM -
Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
...07-09-2026, 11:10 AM -
Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.
There is no single reason why many patients don’t respond to treatment as expected. Cancer is...07-08-2026, 05:17 AM
Comment