Hello Liesbeth,
Hopefully you are no longer having this problem, but we wanted to
follow-up. From our view of your account, all histories are accessible
on the Main public Galaxy server at http://usegalaxy.org.
Our sincere apologies for transient usage issues that occurred around
the time
Hi,
Although I am occupying 91% of my space on the Galaxy platform, since Galaxy
was out, I cannot access my history anymore. No error message appears. What can
I do?
Best regards,
Liesbeth
___
The Galaxy User list should be used for the
I am using Deeptools at the main public server and was adding some files
initially to test. Now I have removed all my files (hidden and unhidden)
and history, but my usage is still at 38%. How can I remove all the files
to have a 0%?
My user name is alexandre.gaspar.m...@gmail.com
Thanks.
A
Hello,
Please check all histories and shared histories. All data must be
permanently deleted, and no histories shared with you, to reach 0% usage.
Find all in the in the history menu under:
* Saved histories - Advanced search - status = all or deleted'
* Histories shared with me
Help is
Hello Nancy,
The attribute sounds as if it is the correct place in the reference
annotation file (the 9th field), but perhaps there are other
format/content problems with the file. Do you have a tss_id? Do you have
exons labeled?
This is the area of the manual that covers the formatting and
Hi Jennifer,
I did see tss_id in my results and also exon labels. The tss_id was
assigned during the calculation, having the numbers tss1, tss2, etc. By
saying writing codes I mean such as in the link you sent to me, there is:
*Note: *If an arbitrary GTF/GFF3 file is used as input (instead of
Hi Nancy,
It is not quite clear in which steps you used the reference annotation
or how these attributes were lost exactly. Cuffcompare is a tool in
Galaxy - but before we go any further I think that examining the history
would be the speedest path to a solution. Would you share a history
Hi all,
I've been trying to use the cufflinks-cuffmerge-cuffdiff flow to analyze my
RNAseq data. However, cuffmerge lost my p_id. My p_id was originally from
changing the protein_id to p_id by myself in the gtf file. The current p_id
showed up in the same attributes column as gene_id in the gtf
Dear Sir or Madam,
Recently I was trying to use Galaxy for my data analysis but ran into
problems.
Condition:
I used galaxy server at PSU.
I tried load local .bam file directly to galaxy, I also tried FTP, but both
ways resulted into the same outcome.
The .bam files I was using are pure
Hello L.Y.,
I just tested .bam upload using FTP (with the client FileZilla) and all
went fine. Just to confirm, you are using the public Main Galaxy server
at http://usegalaxy.org? Many of our services were down for several
hours yesterday for maintenance related reasons - if you upload
Hi,
Can anyone tell me if the ability to randomly sample a sam or bam file
(view -s) is available via Galaxy samtools? I can't find it but it might
be an option that I am missing.
sincerely,
Robert Jackman
rais...@gmail.com
rjack...@bu.edu
Hi Robert,
This function is not wrapped into a tool yet by the dev team. I checked
the Tool Shed as well and didn't see it there. But there is another
option to get to the same result.
The tool Text Manipulation - Select random lines from a file can be
used with a SAM file. Don't not use
On the FastUnifrac webside available at the begining of the year I was able to
obtain p-values having
“unifrac_env.txt”file,
GreenGene Core as the reference tree
and “Automatically generate category mapping file” option was previously
available.
Can I have access to the previous
Hello Vioricia,
For this question, it would be best to contact the team that is hosting
the public Galaxy site, as these are tools custom to their server. The
contact information is on the bottom of the home page:
http://unifrac.colorado.edu/
Best!
Jen
Galaxy team
On 9/25/13 1:13 PM,
Hello everyone,
I found regular expression could be available in the tool (filter and sort)
-Filter. I wonder whether it could be the same in the tool (Text
Manipulation) -Compute. I have checked that the fuction len(c4.split('_'))
would return error. So, could anyone tell me if it was
Hello,
There are some tools in the group 'Text Manipulation' that do this sort
of manipulation directly. Combined, many basic unix functions can be
performed. Combine them to create custom tools using Workflows - even
place them in your tool menu for seamless access.
To move from file A to
Dear Jen,
I am not much of a Galaxy user yet. Some days ago I know something about Galaxy
and found it a really wonderful tool. And I am confused by a simple question
regarding how to extract intron sequences from [gtf file];
Here is a simple of a gtf file:
1 Cufflinks transcript322
Hello Larry,
The Manipulate Fastq tool only brings up the regular trimmer tools
again once sequence and trim are selected, so this will not work. And
a regular expression could be used as a filter, but that will not
actually trim the data.
If you choose to filter, this regular expression
Hi
Is it possible to trim a variable number of a specific nucleotide from the
3' ends of fastq RNA reads? The Manipulate Fastq utility in Galaxy may
have this ability but I do not know how to create a custom inquiry.
Thanks in advance for any assistance.
Larry
You could use the adaptor clip with e.g. a custom poly-A 'adaptor'
its in FASTX-Toolkit for FASTQ data
best,
ido
On Jul 28, 2013, at 8:44 PM, Larry Simpson larrys3...@gmail.com wrote:
Hi
Is it possible to trim a variable number of a specific nucleotide from the 3'
ends of fastq RNA
Dear galaxy members,
I have a question on the databases used in megablast module from galaxy. There
are four db options to blast against with -
1. htgs 28-Jan-2013
2. nt 28-Jan-2013
3. wgs 28-Jan-2013
4. phiX174
Is there any further information to guide which database
Hi Kathryn,
These first three are three different types of sequence databases
available from GenBank The last is a genome assembly for the phiX174 genome.
Information about all can be found here:
http://www.ncbi.nlm.nih.gov/genbank/
There are many uses, one example is covered in our
Hello Kathryn,
Trackster is the primary data visualization tool and can be accessed
by clicking on the mini graph icon within a dataset:
or by going to "Visualization" in the upper menu bar and starting a
new track browser.
hello,
My subject is at the border between Galaxy and Condor
I'found method to use Galaxy with condor cluster solution.
In fact I have wrote a script when Galaxy call clustalw2 , it calls in
fact a script called clustalw2.
All run exactly as I want excepting ... but Galaxy get in error and
Hi Sandra,
Galaxy can certainly be used to correlate a set of unknown genomic
coordinates with another annotated set of genomic corrdinates, such as
those available from UCSC, Biomart, etc.
The tool set to look at is Operate on genomic intervals and an example
of how these tools are used,
Hi
My name is Sandra and I'm a curator of a database of transcriptional
relationships in yeast. We are doing our annual update, and in one paper I
found a number of ChIP-seq results. Unfortunately, the authors only included in
the supplemental information the genome coordinates, but no
Dear Galaxy members,
I am new to galaxy and just installed galaxy on aws cloud. I am testing how it
works and have the following question below:
1. I tried to test bowtie2 with the dataset I uploaded, however, the
window for reference genome is very narrow and nothing from pull-down
Hi Mathew,
Regarding 1 you might want to read this thread:
http://user.list.galaxyproject.org/Problem-with-Depth-of-Coverage-on-BAM-files-GATK-tools-td4654147.html
All tools from GATK are limited to hg_g1k_v37 as far as I know.
Best,
Carlos
On Mon, Aug 6, 2012 at 10:30 AM, Mathew Bunj
Hello Mathew,
Carlos is correct the the tools in the group NGS: GATK Tools (beta)
will require that the data is mapped/associated with the reference
genome hg_g1k_v37. Belinda has offered to help with the details that
go beyond Galaxy and that is great - the GATK forum is definitely the
best
Hi Kanwar,
I found that you also posted this question and another like to the
Google group for SICER on 7/10 and received some help there:
http://groups.google.com/group/sicer-users
Glad that you were able to get the questions resolved. For others
reading this post or interested in SICER
I used SICR to call peaks and have following out put files:
1. test.1removed bed
2. control1 removed .bed
3. test w 200 graph
4. test w200 normalized graph
5. test w200-G600 FDR.05 island.bed
6. test w200-G600 FDR .05 island filtered.bed
7. test w200-G600 FDR .05 island filtered normalized.wig
Hi Qianli,
It looks as if you are using the Extract DNA tool? GTF/GFF files have
coordinates with a 1-based start position - and this was your input, but
the output from this tool produces coordinates with a BED-style 0-based
start position.
The genome index files used by the tool are in
Hi
I want to fetch sequence from soybean genome, according to a gff file. My
gff3 file and genome file are attached to the email, because it is not easy
to recongnize the format if I paste it in the email. And it keeps
reporting the error:
An error occurred running this job: Traceback (most
I have run a ChIPseq work flow in galaxy, At teh end I ran CEAS: Enrichment
on chromosome and annotation (version 1.0.0) to annotate the peaks
which gave me a pdf file shoiwng distribution of peaks across genome with
pie chart as well as well as histogram. It shows that ~5% of my peaks in
5UTR
I have a question about megablast, I want to megablast my seq:
the databases mentioned include (against target databases):
htgs27
nt27
wgs 09
phiX174
How can I find details about these databases and which one is human or
mouse or may be best for my case.
Thanks
Vasu
Hello Vasu,
These databases contain sequences from all species in the divisions. The
number indicates the release version. The actual source is:
ftp://ftp.ncbi.nlm.nih.gov/blast/db/FASTA/
A description of each division's contents can be found at:
http://www.ncbi.nlm.nih.gov/genbank
The
Hello Shamsher,
Another user posted that they have started a Galaxy wrapper for the
Circos tool itself, but I wanted to let you know about the tool EMBOSS
- cirdna: Draws circular maps of DNA constructs.
The link on the tool's form points to all of the EMBOSS tools, including
this specific
If I may add, I believe galaxy will uncompress your files if zipped.
Unzipping a 13 GB file, will take a while.
Kev
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at
Hello,
Recently i have used galaxy to find corresponding amino acids to a list of
SNPs that i have. i used aaChange tool from the tool panel for this
purpose. After obtaining the result i checked the correctness of this
results by searching dbSNP for randomly chosen SNPs. however, some of those
Hello Maha,
This does sound very strange. Would you please share a link to your
history so that we can examine the data and determine where the problem
originates? Please note which dataset contains this particular problem
if there are several runs from this same tool.
Use Options - Share
Hi Shamsher.
We have a small initial wrapper for circos. Its not complete yet and we
are not sure if its even possible to wrap such a complex tool in a good
galaxy UI. But if you are interested i can share our code.
Cheers,
Bjoern
I wonder if is it possible to visualize mutation data in
I wonder if is it possible to visualize mutation data in circular plot
termed as circos plot e.g
@http://www.eurekalert.org/multimedia/pub/31019.php?from=181881
Any suggestion for an alternative tool will also be appreciated.
Thanks
Shamsher
I recently tried to upload a custom made index for bowtie using Filezilla
as my FTP source, but I got an error message, I think due to the autodetect
for file type not recognizing this file type. Is there something special
that I should do to upload my six .ebwt files for my reference?
Hello William,
To use a custom reference genome, all you need to upload is the single
fasta file for the genome. Galaxy will do the rest and create indexes as
appropriate.
Hopefully this helps!
Thanks,
Jen
Galaxy team
On 2/6/12 11:51 AM, William Light wrote:
I recently tried to upload a
Hello,
I'm using the Galaxy Main --I was trying to groom data that I had uploaded at
about 11 AM EST and Galaxy informed me that I had met my quota. Indeed it said
that my quota was 98% full, but my history (my only one) said that I had about
13 Gb-- I deleted everything in my history in
Hello Michael,
Data will count towards the disk quota when not permanently deleted.
Also, once permanently deleted, it will take a bit of time (less than an
hour to several hours) for the disk counts in the UI to update. Perhaps
this has already been resolved, but if not, hopefully the rest
Hi Rahul,
This is the maximum number of bases which can have their score not included
when calculating the result of the selected aggregation function.
For example, if you had a 5 base window with scores of 5,5,2,5 and 5, set
aggregation to min score with a specified value of 4, with the
Hello,
I am running Galaxy locally and it has been performing flawlessly! I
wanted to get more insight about this flag in the FASTQ Quality Trimmer
program:
Maximum number of bases to exclude from the window during aggregation
Does it mean the number of 5' bases to exclude while the doing
I am trying to compare two genetically different strains that I have
sequenced using SOLiD. I was trying to ask where these two strains are
different, either in terms of deletions or polymorphisms, and one idea I
had was to use Bowtie to create an index from one of these strains and then
to map
Hi,
I uploaded a bed file to Galaxy and did some text manipulations. I want to
download the new file as a bed format that I can then open up in excel or a
text editor. However, when I save the data, it is a .tabular format that I
cannot open with these programs. What should I do?
Thanks,
On Thu, Nov 10, 2011 at 6:10 PM, Rena Zheng rzh...@mail.med.upenn.edu wrote:
Hi,
I uploaded a bed file to Galaxy and did some text manipulations. I want
to download the new file as a bed format that I can then open up in excel
or a text editor. However, when I save the data, it is a .tabular
Hello Xaingmimg,
When you uncompress the archive locally, does it contain a single file
with more than 5000 reads? The consistent results and even number of
reads (5000) may mean that the archive contains more than one file.
Currently, Galaxy will only load the first file in an archive.
You can download DRA files directly by FTP to Galaxy . .
Just paste the FTP address directly in the file box when using upload from
my computer
Best
Simon
On 7 November 2011 04:54, Xiangming Ding din...@ucla.edu wrote:
Hi galaxy
I am a new user of galaxy. i met a problem and didnot find
Hello Xiangmimg,
Data files can be loaded using a URL on the Get Data = Upload form.
FTP and HTTP connections are supported. This is briefly described on
that form.
If you are still having issues, there may be a problem with file
compression or the connection. Downloading locally then using
Hi
the file name is spr097786.fastq.bz2.After upload it showed
spr097786.fastq. It showed it only contain around 5000 sequence reads.
I also tried to upload through FTP. so i download the file to my
computer and then upload to FTP in galaxy. the totlal 800M file was
uploaded to the FTP
Hi, I have an Illumina HiSeq lane of sequences, in which I input multiple
samples with 5-prime 6 bp barcodes. The barcodes were added in a way so that
the barcodes are the first 6 bp in the reads. What I need to do is to sort
my reads according to the barcodes, then clip off the barcodes and use
I have read in the mailing list that you have a workflow which can modify
the human GTF file so that it will be compatible with Top Hat. Will it also
work with Ensembl mm9 GTF or there is a different work flow.
Thanks
___
The Galaxy User
Hello,
For tools that allow a custom genome, the form will include an option to
use a Dataset from the history (or similar). Then a sub-menu will pop
up where the reference genome can be selected.
Other basics:
For the query sequences, Fastq or fasta format may be required. After
upload,
Hello Diana,
For the main public Galaxy server, an input sequence file of this size
should not be a problem when analyzed through the standard tools. Hard
quotas are not set at this time, but will be announced soon. Current
guidelines can be found at:
http://galaxyproject.org/wiki/Main
On 09/23/2011 09:26 PM, dtr...@ira.cinvestav.mx wrote:
Hi, mi name is Diana Trejo and I am working with galaxy for first time. I
would like to analyze millions of sequences in galaxy but I don´t know if
it is possible because my file is 330 MB. Are there any MB restriction for
using galaxy?
Hi, mi name is Diana Trejo and I am working with galaxy for first time. I
would like to analyze millions of sequences in galaxy but I don´t know if
it is possible because my file is 330 MB. Are there any MB restriction for
using galaxy?
Thanks for your help
Diana Trejo
--
This message has been
Hi,
I just uploaded the BAM file for an exome sequencing sample and was trying to
use the GATK tools. In the first step, realigner Target creator, I can see my
uploaded file but I can't see any options under the using reference genome
and the following choices so I can't click execute. Did I
Hello Luciano,
This was a bug, fixed in galaxy-central yesterday: changeset
4212f675f95b . You can either pull the changeset into your local
instance or wait for it to be incorporated into the next distribution
(within the next few weeks).
Next time, it would be great if you would send
Hello William,
The tools in NGS: QC and manipulation, especially those in the
sub-section AB-SOLiD data can do the manipulations needed before
mapping. It may be helpful to view the screencast at
http://usegalaxy.org, center pane, quickie #9.
Hopefully this helps to get you started,
Best,
I am trying to use bowtie to assign reads to the s. Cerevisiae genome. I
have data from paired end SOLiD sequencing with two unique six base pair
barcodes. Can I use bowtie to make csfasta and qual files from my mixed
original data split by bar code? I know I can use the trim option to remove
Hi Jackie,
The screencasts under Metagenomic Analyses with Galaxy specifically
use 454 data and would likely be helpful, maybe even if you have already
resolved your prior issue.
http://main.g2.bx.psu.edu/screencast
Apologies for the delay in reply, we were a bit backed up with questions
in
Hi galaxy-users
When trying to display a set of chip microarray data in UCSC main, ,
we encounter this error:
Error(s):
Error line 38879 of
http://main.g2.bx.psu.edu/root/display_as?id=3221463display_app=ucscauthz_method=display_at:
chromEnd larger than chrom chr21_random size (1679928 1679693)
Hello,
The error is indicating that the end of your dataset is larger than the
chromosome it is aligned to for this line (at least). This is expected
when attempting display of certain data types at UCSC.
This is a known issue. You can either remove these lines from your
dataset with tools
Hello Wen,
It's not necessary to send multiple emails to the mailing list; we track
incoming emails to ensure that we respond to all of them.
Your FPKM values do look high, but keep in mind that coverage is only part of
the FPKM calculation; it's also dependent on transcript length and the
Dear Galaxy team and users,
I have a question on the output by cufflinks on Galaxy.
I started with about 28M paired-end reads and mapped them to the reference
genome using Tophat on Galaxy. The aligned fragments were assembled by
cufflinks, again on Galaxy and I got an output with the first
Dear sir,
I was looking through your Galaxy Wiki, but could not find an answer to my
question. I would most appreciate any help regarding the following issue:
I'm conducting a GWAS study in horses. Up until now I've been using PLINK
for my association analysis, and now I wish to generate a
Hi there,
Looking at the output of the SplicingDiff files of CuffDiff, me and my
colleagues are preplexed about the output of the p_values and q_values.
We've tried different inputs of different samples to compare but never seem
to manage to get p_values smaller than 0.50 and we keep getting
Felix,
You seem to be providing the correct inputs to Cuffdiff and it appears to be
producing valid output. More information about setting parameter values and
interpreting Cuffdiff can be found in manual:
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
Good luck,
J.
On Jun 16, 2011, at
What version of Cufflinks is your Galaxy installation running? A recent version
(1.00 and 1.01) had a problem that was causing the splicing and promoter use
tests to have very few differentially regulated genes, according to
http://cufflinks.cbcb.umd.edu/.
-rory
On Jun 16, 2011, at 8:13 AM,
Jagat,
First, a couple housekeeping issues:
(a) the questions you're asking are better suited to the galaxy-user list
(questions about using Galaxy and performing analyses) rather than galaxy-dev
(questions about installing Galaxy locally and tool development), so I've moved
this thread to
Hi,
I have a question for you guys regarding quality filtering.
I have a data set of double MID tagged 454 amplicons, from which I wish to
select high quality sequences above Q20.
The 454 quality filtering system seems to work differently from that given
for the Illumina sequencing i.e. 454
Hey Jennifer,
I was using email/password, just tried again and I got in. Weird. Thanks
for the quick response!
Danny
On Mon, Feb 7, 2011 at 3:21 PM, Jennifer Jackson j...@bx.psu.edu wrote:
Hello Danny,
Are you connecting to main.g2.bx.psu.edu and using your Galaxy credentials
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