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Old 07-20-2009, 06:13 PM   #21
Ka123$
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Is there a way to convert bowtie aligned files to a BED files in unix?
I tried following the directions on the http://vancouvershortr.wiki.sourcefo...tieToBedFormat. But I get a error message.
Please can anyone help?
Do i need to convert the GERALD read into something else????
Do I need to upload a conversion package or something?????
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Old 07-20-2009, 10:22 PM   #22
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If you give me the error you're getting with that file, I can probably fix it for you. People have told me that there is a problem - but no one has told me what the problem *is* yet, and I can't seem to recreate it with the files I have. That might be a quick way of solving your problems.
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Old 07-21-2009, 03:28 AM   #23
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apfejes thanks for the reply,
This might be a very basic problem at the command line as it says command not found....
I am a unix dummy and am playing with this.....
I want to use the convert bowtie to bed in unix and tried typing commands accordingly and did not work....

does it have to be:
./ConvertTobed. GaP_align
is this correct?
Gap_align is the name of the dataset that needs to be converted into BEd file and it is in bowtie aligned format.
Thanks
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Old 07-21-2009, 06:17 AM   #24
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Hi Ka123$,

The first issue is that this is a java command, and requires java to run the command. This shouldn't be a big problem, but it changes the way things are run on a unix system. Jar files are not executable on their own - they must be "fed" into a java interpreter.

With the latest version (4.0.x), the convertToBed.jar application should be invoked as:

"java -jar /path/to/ConvertToBed.jar -input GaP_align --output /output/path/ -aligner bowtie"

You will need to modify the paths to point to the location of the jar file and the desired output path respectively. (You may find you want to use the "-nochr" flag, depending on the nature of your data.)

Full instructions are available at:

http://vancouvershortr.wiki.sourcefo...t/ConvertToBed

ConvertToBed assumes that you're working with Single End Tag data. If you're working with PET data, you'll want to use BowtieToBedFormat.

http://vancouvershortr.wiki.sourcefo...tieToBedFormat

I hope that's enough to get you started! If you still encounter problems, let me know.

Anthony
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Old 07-21-2009, 06:38 AM   #25
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Anthony,

While ConvertToBed is supplied with the Vancouver package, BowtieToBed is not (either 3.3 0r 4.0). Where can one download BowtieToBed?
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Old 07-21-2009, 07:58 AM   #26
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You're correct. Sorry about that oversight. I have added it so that it will be included in the next release.

For the moment, I've attached tarred version of the file. You will need to untar it ("tar -xvf BowtieToBedFormat.tar"), which will unpack the .jar file for you.

I haven't given the built version any run time testing (I usually just run from source), but I'm more than happy to help fix any bugs you might find.

Anthony
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File Type: tar BowtieToBedFormat.tar (40.0 KB, 14 views)
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Old 07-21-2009, 08:27 AM   #27
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Default Boetietobed

Thanks so much Mr.Anthony,
I appreciate your help a lot!
I am a molecular biologist trying out some basic programming . SO thanks to you and everyone else on the forum for the patience and all the input.
I shall try what you mentioned and let u know if I encounter any problems.
Thanks again.
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Old 08-05-2009, 11:24 AM   #28
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I, also, am a molecular biologist dabbling in the ways of the UNIX. Naturally I need guidance as well. In using our neighbor-to-the-north's Vancouver Short Read analysis package (specifically the BowtieToBed converter) I get the confounding error:

Exception in thread "main" java.lang.NoClassDefFoundError: src/lib/ioInterfaces/AlignedReadsIterator
at java.lang.ClassLoader.defineClass1...et cetera

Have I done it all wrong? Am I missing something? I await your sage advice.

Last edited by SeaJane; 08-05-2009 at 11:32 AM. Reason: added specific file
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Old 08-05-2009, 11:40 AM   #29
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Hi SeaJane,

That sounds like a missing dependency in the build - which would be my fault. However, I can confirm that that dependency is satisfied in the latest versions. Could you confirm which version of the package you've downloaded?

Anthony
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Old 08-05-2009, 11:46 AM   #30
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I downloaded version 4.0.2 of the entire package
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Old 08-05-2009, 12:07 PM   #31
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Ok, I've tracked down the problem. I believe this version should fix it for you. The fix will be included in the next release (4.0.4)

Please let me know if you encounter any other problems.

Edit: don't download this file - use the two posts below.
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File Type: gz BowtieToBedFormat.jar.gz (31.4 KB, 5 views)
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Last edited by apfejes; 08-06-2009 at 10:29 AM. Reason: This file does not run to completion.
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Old 08-05-2009, 12:28 PM   #32
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Sorry...I'm still having problems, though it runs a bit further this time ...

Exception in thread "main" java.lang.NoClassDefFoundError: src/lib/Error_handlin
g/GenericProcessingException
at src.lib.ioInterfaces.BowtieIterator.next...et cetera

btw, thanks for being so responsive.
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Old 08-05-2009, 12:42 PM   #33
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Ok, caught that too - it was an inappropriately placed semicolon in the build file. Go figure. I've rebuilt and attached the new file.

Sorry about all of the hassle - I've only used this function a few times before moving away from bowtie, so I hadn't done anything with the compiled version of the code (which was only recently added to the buildout process). Again, if you see anything fishy with the application, please let me know!

Anthony
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File Type: gz BowtieToBedFormat.jar.gz (32.0 KB, 38 views)
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Old 08-06-2009, 01:43 PM   #34
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Thank you! It works well now. By the way, what program are you using now?
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Old 08-06-2009, 03:26 PM   #35
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Hi SeaJane,

I'm glad it's finally working, and sorry that it was such a hassle to get it to that shape!

Mostly I'm working with Maq, but I'll be putting BAM/SAM readers into the project shortly. BWA here we come....

Anthony
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Old 12-01-2009, 08:28 AM   #36
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Hi apfejes,

I got a problem with using the ConvertToBed.jar in a redhat system. I tried to convert from Bowtie to Bed (some mysterious reason also happens when I tried to use the sam2bed.py script on the site but it is a different problem...). when i ran ConvertToBed as:

[root@my lab conversion_util]# java -jar ConvertToBed.jar -aligner bowtie -input /some input dir/input.txt -output ./output -name Name

It reports:

Exception in thread "main" java.lang.ClassFormatError: src.fileUtilities.ConvertToBed (unrecognized class file version)
at java.lang.VMClassLoader.defineClass(libgcj.so.7rh)
at java.lang.ClassLoader.defineClass(libgcj.so.7rh)
at java.security.SecureClassLoader.defineClass(libgcj.so.7rh)
at java.net.URLClassLoader.findClass(libgcj.so.7rh)
at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
at java.lang.ClassLoader.loadClass(libgcj.so.7rh)
at gnu.java.lang.MainThread.run(libgcj.so.7rh)

Could you help on this? Thanks a lot.
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Old 12-01-2009, 02:31 PM   #37
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Hi heculase,

The error you're showing is a java error, and not something to do with the jar file itself... The most recent versions were all compiled for Java 1.6 in order to support Picard (for SAM/BAM formats), and this is probably just be an indication that you need to upgrade to the latest java.

Unfortunately, I'm currently away this week, but I can take a look when I get back if Java 1.6 doesn't solve your problem.

Anthony
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Old 12-02-2009, 07:47 AM   #38
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Thanks a lot Andy. It is indeed a java version problem. I updated to 1.6 and it worked great. Thank you very much!

heculase

Quote:
Originally Posted by apfejes View Post
Hi heculase,

The error you're showing is a java error, and not something to do with the jar file itself... The most recent versions were all compiled for Java 1.6 in order to support Picard (for SAM/BAM formats), and this is probably just be an indication that you need to upgrade to the latest java.

Unfortunately, I'm currently away this week, but I can take a look when I get back if Java 1.6 doesn't solve your problem.

Anthony
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Old 01-24-2010, 07:41 AM   #39
bora
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Default bowtie to .gff and .wig

Quote:
Originally Posted by graveley View Post
Dear Yogesh,

We do this by writing a perl script that reads in the alignment information and writes a new file in the appropriate format. I would send you what we use, but we do not use export.txt files. We are currently doing alignments with Bowtie and then converting the output to .gff and .wig files.

Brent
bowtie to .gff and .wig

Dear Brent,
As the users before me I would also appreciate the pearl script for the bowtie alignment files to .wig and .gff. Thanks a lot. My email is:
bora-bora@volny.cz
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Old 01-24-2010, 10:23 AM   #40
quinlana
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If it helps, there is a generic BAM to BED utility (bamToBed) available in BEDTools (bedtools.googlecode.com).

Aaron
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