[SeaJane]

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.

[Ka123$]

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.

[apfejes]

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

[kmcarr]

Anthony,

While ConvertToBed is supplied with the Vancouver package, BowtieToBed is not (either 3.3 0r 4.0). Where can one download BowtieToBed?

[apfejes]

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.sourceforge.net/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.sourceforge.net/BowtieToBedFormat

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

Anthony

[Ka123$]

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

[apfejes]

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.

[Ka123$]

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?????

[Ka123$]

HI Brent,
My email is [email protected]ks
What kind of format are (GERALD) aligned output files?Aligned files are mapped files I suppose......just two terminologies.....?

[Ka123$]

Bowtie to Bed files

Hi Brent
could you also help me with the perl script to convert bowtie to BED? I am not a perl person. Also can find peak convert the bowtie-align files to a cisGenome compatible file?
THanks
Ka

[joseph]

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

Hi Brent,
I would really appreciate it if you send me your perl scripts for conversion of bowtie output to .gff and .wig files.
my e-mail: [email protected]
Thanks
Joseph

[kmcarr]

Layla,

For the score I would use the mapping quality (column 7 of the MAQ .aln file). Phase is meaningless in this context, it only applies to coding sequence features. In your case just put a '.' in column 7.

[Layla]

maq to GFF2 format

Hi,

I know this is quite an old thread but useful for me at this moment.
Searching for a method to convert a maq alignment (to human ref genome) output from me-dip seq to GFF2 format for batman but no luck so far. Is there a script already available for this or is there a conversion tool to do this?

GFF2 example:
col1 col2 col3 col4 col5 col6 col7 col8 col9
Chr1 Homo_build36 Reference 1 45 . + 1 Sequence1

How does one define column 6 (score) and column 7 (phase) from the maq alignment file?

Help appreciated

L

[alperyilmaz]

R package from BioConductor

There's another R package to be released, which will be available thru BioConductor. It's mentioned in a recent workshop. The workshop material can be viewed here.

[apfejes]

That's correct - The code is currently in development, but should be ready shortly. (I hate saying that about software, but a lot of the code has already been written.)

Cheers,
Anthony