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Old 02-17-2010, 08:21 AM   #41
genbio64
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@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,
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Old 02-17-2010, 08:26 AM   #42
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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.
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Old 02-17-2010, 08:32 AM   #43
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@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

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Old 02-17-2010, 08:39 AM   #44
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Hi Genbio,

Thanks for the information, however, what I'm actually looking for is the error you're observing. If it's caused by java, it should give information about where in the code the error occurred, or which module caused the error. Since I know nothing about the file you have or the operating system you're using, the best information that would help me solve your problem is the error thrown by java itself, which normally gives a clear indication of what was happening when the fault happened.

Cheers!
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Old 02-17-2010, 08:41 AM   #45
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It did not give a java specific code, only
"Error: coundn't creat log file:"
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Old 02-17-2010, 08:47 AM   #46
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That Error, I am familiar with. It means you've either given it an invalid output directory, or do not have permissions to write to that location. You'll either have to check the output directory you've provided to make sure it exists (it will not be created, if it does not exist), or to make sure that the the permissions are correct and you are allowed to write to the directory you have specified.
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Old 02-17-2010, 09:11 AM   #47
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That's off b/c all of the file permission are fine. When I run the command the log file is created but is empty. Could I use the BowtietoBed.jar command instead, even though my data is not paired end reads?

cheers,
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Old 02-17-2010, 09:23 AM   #48
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Well, I'm not sure what the problem is, then. I haven't ever seen that error being given for any other reasons than the ones I've suggested. If you could cut and paste a few lines before the error occurs, maybe I can figure this out.

As for using BowtietoBed, the whole suite of tools uses the same underlying log file code, so if it's not working for one, it probably won't work for any of them.

That said, you could try to use it with the -noflag option, and is might work - I haven't tested it under those conditions, so I can't guarantee it.

Anthony
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Old 05-20-2010, 05:05 AM   #49
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Hi Anthony.
First of all, thanks so much for providing support for Convert To BED and other algorithm's over here.

I also came across the error above, and indeed it was a permissions issue. Somehow the folders in my Vancouver package extraction were "read only", so this discussion has already been very helpful to me.

I have another question; Is there a way to make ConvertToBED output to a single file instead of a separate file for each chromosome?

Thanks!
Miltron / Erna Magnúsdóttir, University of Cambridge
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Old 05-20-2010, 07:14 AM   #50
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Hi Miltron,

Unfortunately, there isn't. This is simply because it was the easiest way to do the sorting required by other applications in my suite, back when the standard alignment formats weren't guaranteed to be anywhere near sorted by chromosome or position.

However, combining all of the beds back together is a simple matter of unzipping and concattenating the files:

gunzip *.gz
cat *.bed > output
mv output allchr.bed

Cheers,

Anthony
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Old 07-14-2010, 02:19 AM   #51
Anou
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Default textfile to gff/gbk

Hi everyone,

I have a nucleotide sequence of taro (26S to 18S Intergenic Spacer from taro (Colocasia esculenta). It was analysed by a student so its just a textfile and not published in ncbi or similar websites yet. I need it in gff or gbk format. Any idea how to convert it?

Regards, Anja
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Old 07-14-2010, 11:20 AM   #52
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I doubt there are any generic "text file to *" converters out there. If the text file had a format such as bed, we might be able to point you in the right direction.

for the moment, your best bet is to write your own converter - and hope that you haven't lost a lot of information that you'd need to complete the gff format requirements - or to track down the original files of the sequencing/aligning results.
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Old 07-14-2010, 12:54 PM   #53
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thanks
i got it now in gbk and fasta. unfortunatelly i couldnt convert it to gff/gff3. i tried the perl script bp_genbank2gff3.pl... but got this error:

# Input: taro.gbk

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: asking for tag value that does not exist organism
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
STACK: Bio::SeqFeature::Generic::get_tag_values /usr/local/share/perl/5.10.1/Bio/SeqFeature/Generic.pm:517
STACK: main::gff_header /usr/local/bin/bp_genbank2gff3.pl:895
STACK: /usr/local/bin/bp_genbank2gff3.pl:406

does anyone know what that means?
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Old 04-22-2011, 10:28 PM   #54
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Default Format conversion

Hello sir,

I want to convert the fasta sequence that I have to GFF format. Please help me , how should I convert it......
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Old 08-31-2011, 11:08 PM   #55
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Default perl scripts for conversion of bowtie output to .gff and .wig files

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

Hi Brent,
I would really appreciate it if you can send me the perl scripts for conversion of bowtie output to .gff and .wig files.
my e-mail: parveendabas@gmail.com

Thank you
Parveen Dabas
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Old 09-09-2011, 12:49 PM   #56
diya
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Default bed to wig format

Hi,

I am looking for some tool which can convert the bed files to wig files or bowtie output to directly wig format?

Thanks,

Diya
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Old 01-19-2012, 08:26 AM   #57
dzavallo
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Default bowtie output file

Hi, I have a question about bowtie output.
I have to converte the output file to .gff in order to use it in the GBrowser.
Is there a way to convert .sam to .gff directly?

The output file in bowtie only give the first coordinate of the mapping, but .gff file require both.
(Chr2 20000 20021) if it was the case of a miRNA for example

Does anyone know if bowtie have that output option?

Thanks!

Diego
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Old 06-30-2014, 05:01 AM   #58
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You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html
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