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 of
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
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
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
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 with
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 th
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 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 fi
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
overl
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 .ba
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
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
___
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, B
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 webs
Hi Jen,
Thank you for your help. The Galaxy tools can do many things!
From: Jennifer Jackson
Sent: Friday, August 30, 2013 8:31 AM
To: 师云
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Question about expression in Galaxy tools
Hello,
There are some tools in the group '
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
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 pos
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
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 wrote:
>
> Hi
>
> Is it possible to trim a variable number of a specific nucleotide from the 3'
> ends of fastq RNA reads? The "Manipula
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
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 Metagenom
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 woul
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.
http://wiki.galaxyprojec
Dear galaxy group,
I have question on the data visualization from output of galaxy pipeline. Is
there any ideogram tool inside of galaxy?
Regards,
Kathryn
___
The Galaxy User list should be used for the discussion of
Galaxy analysis an
Hello,
I've moved this over to the galaxy-dev list since it concerns a local
installation.
You'll want to use the 'condor' job running plugin, which is provided with the
Galaxy distribution. Have a look at the job_conf.xml.sample_advanced file to
see how this would be configured.
A very basi
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 informat
Kathryn,
Are you using the galaxy cloud configuration provided by the team, or have you
installed your own galaxy on a cloud instance?
It sounds like the latter, in which case you'll need to configure reference as
detailed here: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup. You
may
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 menu
That is correct, I was able to standardize the work flow, which can be a
starting point for others. I can add to Galaxy shared addition, so that
others may not waste time in looking at what I was searching (at least).
Thanks
On Tue, Aug 7, 2012 at 12:59 PM, Jennifer Jackson wrote:
> Hi Kanwar
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 det
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
b
Hi Mathew,
If you are new to the GATK tools you may want to read some of our
introductory materials at this link:
http://www.broadinstitute.org/gatk/guide/topic?name=intro
You will find some documents explaining what input files you can use, what
are the constraints, and plenty of information abo
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 wrote:
>
I have been trying to use either Unified genotyper or Freebayes on one of the
Bam file. Both are failing.
1. With Unified genotyper it give me message saying Sequences are not currently
available for specified build. I have hg19 related data and using default
settings (pick up hg_g1k_v37 no
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
8
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 .2b
Hello Qianli,
This appears to be the same data as submitted as a recent bug?
Converting the query coordinates to BED format is still the
recommendation. This should be a good solution for most, if not all, of
your prior Extract tool failures and is a good method overall.
First "Convert Form
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 rece
Hello,
It sounds as if you are using the Cistrome hosted Galaxy instance? If
so, it would be best to contact them directly to discuss the
tools/wrappers developed by their group. This is the primary web site:
http://cistrome.org. A help email is on the Cistrome Galaxy's login page.
Good luck
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 regi
Hi Kanwar,
A simple way is to just treat the SAM dataset as a text file and perform
some counts similar to those in this tutorial:
https://main.g2.bx.psu.edu/u/aun1/p/galaxy101
The basic outline would be to:
1 - remove unmapped with Filter SAM, "The read is unmapped", "no"
2 - convert sam -> i
I have a sam file after running BWASW and want to extract unique
(alignments that are aligning once to genome) from this sam file. I read in
other posts that I may be able to use Sam tools> filter Sam option to
filter the said flag on wise flag. However I could not find whether I have
to use defaul
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 except
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 Maha,
Currently, the aaChanges tool accepts SNP input data in a format such as:
chr22 15660821 15660822 A/G
chr22 15825725 15825726 G/T
chr22 15827035 15827036 G
Where all of the SNP strings are reported with respect to the (+)
strand. In your input dataset, the coordinates are
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 specifi
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
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
SNP
If I may add, I believe galaxy will uncompress your files if zipped.
Unzipping a 13 GB file, will take a while.
Kev
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegal
Hello Elwood,
Just to double check (although you have probably already seen it), when
using the FTP client, the same basic steps from this wiki were followed?
Also please that you can FTP compressed data:
http://wiki.g2.bx.psu.edu/FTPUpload
Moving data from the FTP transfer area on the "Get
Hello:
I apologize for bothering you but I am just beginning to work with mRNAseq
data and it appears as though Galaxy will be quite useful but I suspect,
even after looking some of the tutorials that I will be either making
mistakes or just not have a good sense of things.
I used "Fetch" off a ne
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 circul
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
Hi William,
To be sure that we are talking about the same thing, you are trying to
use a custom reference genome with Bowtie? As the target genome? If so,
then what you want to load is a fasta file of the
chromosomes/scaffolds/contigs that represent that species, for a
particular genome build
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 cu
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 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 of
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 orde
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 actio
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 th
On Thu, Nov 10, 2011 at 6:10 PM, Rena Zheng 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 format that
> I canno
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,
Ren
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 my
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.
Hope
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 su
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 usi
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 wrote:
> Hi galaxy
>
> I am a new user of galaxy. i met a problem and didnot find similar
> questio
Hi galaxy
I am a new user of galaxy. i met a problem and didnot find similar
question in FAQ. I wanted to upload the data from DDBJ DRA dataset to
galaxy through UTL method. The file is around 800M. However after
uploading, the FASTQ file was just around 2M. So I wanted know whether
it is
Hello,
The tool documentation provides some help for this:
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff
Basically, the ".combined.gtf file produced by Cuffcompare" is the
preferred input, but it does depend on how Cuffcompare was run, as
explained in the manual.
Questions about this t
Hi,
I am confused about the first line in cuffdiff (using Galaxy on the cloud,
not sure if it's different for local instances). It reads:
Transcripts:(choose a file)A transcript GTF file produced by cufflinks,
cuffcompare, or other source.
What file should I load here? I have 4 groups of 2-4 r
Hello Tracy,
In the group "NGS: QC and manipulation -> FASTX-Toolkit for FASTQ data"
there are two tools "Barcode Splitter" and "Trim sequences". Use the
first tool, then the second. Instructions are on each tool's form and
details are at the FASTX-Toolkit web site (link is also on the tool fo
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 th
Hello,
The workflow is available at this location:
http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq#faq5
The workflow specifically modifies Ensembl chromosome labels in a GTF
file to be UCSC chromosome labels by adding a "chr" to the names ("1" ->
"chr1"). This type of change is
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 lis
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,
I WANT TO ALIGNMENT MILLIONS OF SEQUENCES FROM A sRNA LIBRARY WITH A SMALL
GENOME (2600 BASES). HOW CAN I DO THIS ALIGNMENT IN GALAXY?. I HAVE TRIED
WITH MULTIPLE ALIGNMENTS FROM TOOLS, BUT I CAN NOT SELECT BOTH FILES.
THANKS FOR YOUR HELP
DIANA TREJO
--
This message has been scanned for viru
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
Hope
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?
Than
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
Biology Building
> University of Iowa
> Iowa City, IA 52242
> (P) 319-335-0266
>
> From: Daniel Blankenberg [mailto:d...@bx.psu.edu]
> Sent: Thursday, August 18, 2011 12:19 PM
> To: Hong, Xiaojing
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] question a
Hi Xiaojing,
You'll need to make sure that the dbkey of your input BAM file is set to a
genome build that has data available. Click the pencil icon to set the genome
build. If you have set the genome build, but still have an empty select box
then data may not be available for this build/tool c
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 quest
I have created fixed-step wiggle files for a project that I am working on,
but I am wondering if there is an easy way to transform the values by a
correction factor to account for differences in in the number of reads for
two different samples (one had 1.5 million or so, the other had 6.6million).
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,
Bes
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
th
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
i
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 i
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=3221463&display_app=ucsc&authz_method=display_at:
chromEnd larger than chrom chr21_random size (1679928 > 167969
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 tota
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 few
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 few
As the tool help says about the input file: "Tabular Data is a tab
delimited header file with chromosome, offset and p values to be
plotted"
In other words if you have a text file containing tab delimited
columns, with a header row and some data you should be good to go.
Attached is a sample that
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 Manhat
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, Fe
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 8:
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 highe
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