I am quite new to RNA-seq analysis, but what I have learned so far is that
replicates are important. If you have this result with no replicates then
P-values are more or less meaningless. You can also gauge what is happening by
looking at the modelled read count output. If the counts are both
Hi Noa,
Yes I did use Cufflinks so this sounds just like my problem. So how have you
dealt with the problem?
Best wishes,
Clare
On 14 Nov 2013, at 18:17, Noa Sher wrote:
> Hi Clare
> We just ran into a similar issue about a week ago and were debugging with the
> authors of cuffdiff
> Appar
Dont use the - b parameter
Sent from my iPhone; please excuse any brevity or typos!
On Nov 15, 2013, at 2:51 PM, clare Hardman wrote:
> Hi Noa,
>
> Yes I did use Cufflinks so this sounds just like my problem. So how have you
> dealt with the problem?
>
> Best wishes,
>
> Clare
>
>
>
> On
Hi Clare
We just ran into a similar issue about a week ago and were debugging
with the authors of cuffdiff
Apparently there are issues with the -b parameter - were you using
this in cufflinks?
If yes - this may be the cause - we switched the order of the
replicate
Hi Cory,
A list of Galaxy dependancies can be found on the wiki at:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
...although many tools allow a range of tool versions.
You can also identify the information about the specific tool versions by
clicking on the View Details Œi¹ icon o
look forward to the update, will that mean another version of Cuffdiff again?
Kind regards,
Johanna
From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu]
Sent: Thursday, August 22, 2013 8:04 PM
To: Johanna Sandgren
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] Cuffdiff changes
I am
> Where can I see which version are being used?
You can see both the Galaxy tool version and the Cuffdiff tool version (when
available) by clicking on the 'view details' icon (the 'i' at the bottom of an
expanded dataset). Right now the Cuffdiff version is not displayed, but that
will change wh
> I am wondering why Cuffdiff suddenly gives many more significant DE genes?
Cuffdiff was recently updated to version 2.1.0; this update likely explains the
different results that you see.
> I have rerun several analysis, also with more samples in each group, all give
> much more significant ge
Thanks for the information.
I've added an option to the Cuffdiff tool so that the read group files can be
output by Galaxy; this should make it possible to run Cuffdiff in Galaxy and
then Cummerbund for replicate analysis. This change will make it out to our
public server in a couple weeks.
T
In the past, others have had success using Cummerbund with Galaxy, and there's
even a Cummerbund wrapper in the tool shed:
http://toolshed.g2.bx.psu.edu/view/jjohnson/cummerbund
That said, it appears that replicate information is largely contained in the
read group tracking files, which are no
> The header of the Cuffdiff tool page says it is version 0.0.5
This version is the Galaxy tool wrapper version, not the tool version. (Yes,
this is a usability issue.) You can find the tool version in the dataset's
information panel by clicking on the 'i' icon.
> Is there a way, or setting, on
Hi Jeremy,
The header of the Cuffdiff tool page says it is version 0.0.5
Is there a way, or setting, on Cuffdiff 2.0 to revert the parameters to be
more similar to Cuffdiff 1.3?
Cheers,
Mo Heydarian
PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe
This is likely due to the upgrade from Cufflinks 1.3.x to Cufflinks 2.0.x;
Cufflinks 2.0 introduced a new algorithm for Cuffdiff in particular. You can
read about these changes on the website:
http://cufflinks.cbcb.umd.edu/ (and there's a manuscript describing the changes
as well).
You might co
We are having the exact same issue, on the main server and our (recent)
cloud instances.
Were some of the hidden Cuffdiff parameters modified since fall 2012?
Cheers,
Mo Heydarian
On Mar 13, 2013 11:02 AM, "Jenna Smith" wrote:
> Hi,
>
> I'll preface my concern by saying that I'm a novice to Cuf
Hello Wei,
The results do sound strange. The best advice to start with is to make
sure that you are up-to-date with both Galaxy and the RNA-seq tools and
using the best possible inputs.
1 . Make sure that you are running the latest distribution
http://wiki.galaxyproject.org/DevNewsBriefs
Use the replicates option (yes, a bit of a misnomer) and put each Tophat run in
its own group. This will produce a tabular file with FPKM for each group/run.
Best,
J.
On Nov 12, 2012, at 10:05 AM, Vevis, Christis wrote:
> Hi,
>
> I got confused while trying to perform Cuffdiff for my RNA se
Hello,
Thank you for sharing your history. The difference in FPKM values can be
explained by the use of the -N option ("Perform quartile normalization:
Yes"). Set this to "No" to avoid the variable per-run normalization.
This has also been discussed at seqanswers.com:
http://seqanswers.com/fo
ib,
Look at the status column. I suspect that for this example you given
the status is HiData. Cuffdiff considers the expression are very high
and no statistic testing would have been done for the gene. fpkm 2=0
could be misleading, as it may not be actually 0. I have encountered in
a data
Hello,
Would you be able to share a history containing these data? Use
"Options (gear icon) -> Share or Publish", generate the share link, then
copy and paste that into a reply email sent to me directly. Please note
the dataset #'s for the Cuffdiff runs that you are comparing and make
sure th
On Wed, Oct 3, 2012 at 7:35 AM, Ross wrote:
> On Wed, Oct 3, 2012 at 9:11 PM, i b wrote:
>> Dear all,
>> how reliable is running Cuffdiff without replicates? e.g.one samples
>> agains another one?
>>
>> Is it statistically makign any difference when using replicates?
>
> Seqanswers might be a bet
On Wed, Oct 3, 2012 at 9:11 PM, i b wrote:
> Dear all,
> how reliable is running Cuffdiff without replicates? e.g.one samples
> agains another one?
>
> Is it statistically makign any difference when using replicates?
Seqanswers might be a better place to ask this very interesting
technical questi
Hello,
A very similar question came up a few days ago and Jeremy had some good
advice for how to approach learning to interpret this data:
http://lists.bx.psu.edu/pipermail/galaxy-user/2012-August/004985.html
Best,
Jen
Galaxy team
On 8/15/12 8:49 AM, i b wrote:
Dear all,
in cuffdiff output
Hi Yan,
Would you please submit this as a bug report? It helps if you leave all
inputs undeleted in your history. Instructions:
http://wiki.g2.bx.psu.edu/Support#Reporting_tool_errors
Thanks!
Jen
Galaxy team
On 8/16/12 6:18 AM, Yan He wrote:
Hello,
I am having a problem running Cuffdiff o
Sorry, I did not read carefully. All three samples are listed, just
down in the column I found the other sample.
ib
On Sat, Aug 11, 2012 at 7:41 PM, i b wrote:
> Dear all,
> I ran Cuffdiff with 3 groups: A, B, C each with 2, 5 and 1 replicates
> respectively.
> When looking at the transcripts d
Hello Irene,
These are RefSeq transcript identifiers. In some GTF file sources,
transcript_id is also assigned to the gene_id attribute in the 9th
field, which can cause confusion. Alternative GTF sources are Ensembl
and iGenomes. However, examining differential expression at the
transcript l
Hello Irene,
This issue is similar to the original. The input GTF for this run
(dataset #15) has tss_id populated, but not p_id. The p_id attribute is
required for the CDS calculations.
http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff_input
(quote) Cuffdiff Input:
AttributeDescr
Hello Irene,
There appears to be a problem with the information entered into the tool
form for the labels (e.g. "Group name"). The command string only shows
one group label value when there are two group data sets.
You submitted a bug report for this same issue, so I will take a look
there a
Hello Irene,
Yes, this is can be the result if your source GTF data did not have the
full compliment of attributes needed by Cuffdiff to perform these
calculations.
The primary tool documentation covers this information here:
http://cufflinks.cbcb.umd.edu/manual.html#fpkm_track
The iGenome
From: Jennifer Jackson [j...@bx.psu.edu <mailto:j...@bx.psu.edu>]
Sent: Tuesday, July 17, 2012 1:58 AM
To: Irene Bassano
Cc: galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>
Subject: Re: [galaxy-user] cuffdiff
Hello Irene,
On 7/16/12 4:11 PM, Irene Bassano
Hello Irene,
On 7/16/12 4:11 PM, Irene Bassano wrote:
Hi,
just few questions about cuffdiff if anyone can answer:
1.how can I load more than two sam/bam files?Galaxy gives spaceonly for two
files
Change the tool form for the option "Perform replicate analysis:" to be
"Yes" (the default is "
Hi Ateequr,
This post from today has information another member found at
seqanswers.com, directly from the CuffLinks/Merge/Diff tool author:
http://user.list.galaxyproject.org/Re-1-cuffcompare-or-cuffmerge-td4581029.html
Best,
Jen
Galaxy team
On 4/17/12 8:00 AM, Ateequr Rehman wrote:
Dear A
Hi Ateequr,
I don't think there is an easy answer to your question. I would highly
recommend you take a look to this recently released paper from Tophat
and Cufflinks authors:
Differential gene and transcript expression analysis of RNA-seq
experiments with TopHat and Cufflinks.
http://www.ncbi.nlm
Hello Ateeq,
It looks like you are working with a bacterial genome. There has been
some limited discussion on the Galaxy mailing list about using RNA-seq
tools with circular genomes, but the best resources are probably the
tool documentation itself (e.g.
http://cufflinks.cbcb.umd.edu/manual.h
Hello Erin,
This was a temporary problem due to a new filesystem we installed during
this time frame, that has since been resolved. Please try again and if
the problem persists, please send a bug report from the error dataset
using the green bug icon. This allows us to gain access to the input
t; box for
analyses where I provide the fasta and gtf file.
Thanks,
David
-Original Message-
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, August 19, 2011 9:20 AM
To: David K Crossman
Cc: galaxy-user (galaxy-user@lists.bx.psu.edu)
Subject: Re: [galaxy-user] Cuffdiff question
Hello David,
This is a known bug. The correction is planned to be moved out onto the
public Galaxy instance at the next update (within a week).
Sorry for the current inconvenience,
Best,
Jen
Galaxy team
On 8/19/11 7:00 AM, David K Crossman wrote:
Hello!
I have an RNA-Seq project which con
Thanks for the reply. I tried to use the script provided on a previous
galaxy thread for adding the chr on to the gtf file on the mac terminal but
I keep getting this error -
awk: can't open file ensembl.gtf
source line number 1
I am very new to using the terminal so please let me know if there
> Thanks for the reply. I tried to use the script provided on a previous galaxy
> thread for adding the chr on to the gtf file on the mac terminal but I keep
> getting this error -
>
> awk: can't open file ensembl.gtf
> source line number 1
>
> I am very new to using the terminal so please l
Hello Kurinji,
> I was at your USC Galaxy seminar last week, which I found very helpful -
> thank you!
Glad to hear that you found the workshop helpful. As a reminder, please email
questions about using Galaxy and its tools to the galaxy-user mailing list
(which I've cc'd). You may get quicker
>
> this is an example of my CuffDiff gene fpkm tracking file.
>
> tracking_id class_code nearest_ref_id gene_short_name tss_id locus
> q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi
> XLOC_01 - - MT-ND5 - chrM:0-1657112484.
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