[genbio64]

@Apfejes,
I have the Vancouver Short Read package 4.0.1.2 and ran the ConverttoBed command because I have data from single paired end reads. I aligned them using Bowtie and the file had a .txt format. The ConverttoBed command follows:

java -jar conversion_util/ConvertToBed.jar -aligner -bowtie -input bowtie.txt -qualityfilter 10 -output output_dir/my_directory -noprepend

Cheers,

[apfejes]

I've never seen that problem before. Could you provide the full output of the error for me, otherwise I don't know where to begin looking to solve this problem. Java normally gives more verbose errors than that, when throwing an error.

[genbio64]

@Apfejes
I attempted to use the ConverttoBed.jar utility on some Solexa data after bowtie alignment but I received this error:
"Couldn't write to analog file"

Can you please tell me why this occurred?

Cheers,

[quinlana]

If it helps, there is a generic BAM to BED utility (bamToBed) available in BEDTools (bedtools.googlecode.com).

Aaron

[bora]

bowtie to .gff and .wig

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:
[email protected]

[heculase]

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

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

[apfejes]

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

[heculase]

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.

[apfejes]

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

[SeaJane]

Thank you! It works well now. By the way, what program are you using now?

[apfejes]

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

[SeaJane]

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.

[apfejes]

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.

[SeaJane]

I downloaded version 4.0.2 of the entire package

[apfejes]

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