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.
Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
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.
AnthonyThe more you know, the more you know you don't know. —Aristotle
Comment
-
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
Comment
-
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,
AnthonyThe more you know, the more you know you don't know. —Aristotle
Comment
-
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
Comment
-
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.The more you know, the more you know you don't know. —Aristotle
Comment
-
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?
Comment
-
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: [email protected]
Thank you
Parveen Dabas
Comment
-
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
Comment
-
You could also use GenomeIntervals2BED.py script available within the SeqGI framework.
Have a look: http://seqgi.sourceforge.net/Genomeintervals2bed.html
Comment
Latest Articles
Collapse
-
by seqadmin
The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
Channel: Articles
05-06-2024, 07:48 AM -
-
by seqadmin
The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
Channel: Articles
04-22-2024, 07:01 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, Yesterday, 06:35 AM
|
0 responses
14 views
0 likes
|
Last Post
by seqadmin
Yesterday, 06:35 AM
|
||
Started by seqadmin, 05-09-2024, 02:46 PM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-09-2024, 02:46 PM
|
||
Started by seqadmin, 05-07-2024, 06:57 AM
|
0 responses
17 views
0 likes
|
Last Post
by seqadmin
05-07-2024, 06:57 AM
|
||
Started by seqadmin, 05-06-2024, 07:17 AM
|
0 responses
19 views
0 likes
|
Last Post
by seqadmin
05-06-2024, 07:17 AM
|
Comment