SEQanswers

Go Back   SEQanswers > Applications Forums > Genomic Resequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
ALLPATHS: does it work? francesco.vezzi Bioinformatics 35 06-01-2014 05:21 AM
bowtie index problem (bowtie-build and then bowtie-inspect) tgenahmet Bioinformatics 4 09-10-2013 11:51 AM
How to work out coverage? James Bioinformatics 1 09-22-2010 10:29 AM
Various assemblers and getting them to work avtsanger Bioinformatics 1 07-04-2010 10:20 PM

Reply
 
Thread Tools
Old 08-18-2009, 03:09 PM   #1
jamminbeh
Member
 
Location: Los Angeles

Join Date: Aug 2009
Posts: 11
Default Getting Bowtie to work

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 is offline   Reply With Quote
Old 08-19-2009, 07:53 AM   #2
jamminbeh
Member
 
Location: Los Angeles

Join Date: Aug 2009
Posts: 11
Default

the error message is:

make: *** No targets specified and no makefile found. Stop.
jamminbeh is offline   Reply With Quote
Old 08-19-2009, 10:05 AM   #3
jamminbeh
Member
 
Location: Los Angeles

Join Date: Aug 2009
Posts: 11
Default

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?
jamminbeh is offline   Reply With Quote
Old 08-26-2009, 06:34 AM   #4
joa_ds
Member
 
Location: belgium

Join Date: Dec 2008
Posts: 52
Default

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?
joa_ds is offline   Reply With Quote
Old 08-26-2009, 07:37 AM   #5
jamminbeh
Member
 
Location: Los Angeles

Join Date: Aug 2009
Posts: 11
Default

Yes, I downloaded it from that website, and i'm using a unix shell in windows.
jamminbeh is offline   Reply With Quote
Old 08-26-2009, 07:38 AM   #6
joa_ds
Member
 
Location: belgium

Join Date: Dec 2008
Posts: 52
Default

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.
joa_ds is offline   Reply With Quote
Old 09-07-2009, 02:00 PM   #7
Ka123$
Member
 
Location: MD

Join Date: Jul 2009
Posts: 27
Default 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$ is offline   Reply With Quote
Old 09-07-2009, 02:58 PM   #8
Ka123$
Member
 
Location: MD

Join Date: Jul 2009
Posts: 27
Default 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$ is offline   Reply With Quote
Old 09-24-2009, 07:28 AM   #9
Ka123$
Member
 
Location: MD

Join Date: Jul 2009
Posts: 27
Default

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
Ka123$ is offline   Reply With Quote
Old 02-23-2010, 02:32 AM   #10
ikrier
Member
 
Location: Lausanne

Join Date: Dec 2009
Posts: 19
Default

Did you try using eland_extended?
__ you probably solved this, so I wish I could remove my post
ikrier is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:43 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO