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
Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
Channel: Articles
04-04-2024, 04:25 PM -
-
by seqadmin
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...-
Channel: Articles
03-22-2024, 06:39 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 04-11-2024, 12:08 PM
|
0 responses
31 views
0 likes
|
Last Post
by seqadmin
04-11-2024, 12:08 PM
|
||
Started by seqadmin, 04-10-2024, 10:19 PM
|
0 responses
32 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 10:19 PM
|
||
Started by seqadmin, 04-10-2024, 09:21 AM
|
0 responses
28 views
0 likes
|
Last Post
by seqadmin
04-10-2024, 09:21 AM
|
||
Started by seqadmin, 04-04-2024, 09:00 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
04-04-2024, 09:00 AM
|
Comment