To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Cuffdiff output
Hi,
I have a question about interpreting the cuffdiff data and how to pick up
significant genes. I have genes which show ~8 fold change between 2 conditions:
eg from FPKM of 0.08 to 28 and yet they are not significant
Hi,
I have a question about interpreting the cuffdiff data and how to pick up
significant genes. I have genes which show ~8 fold change between 2 conditions:
eg from FPKM of 0.08 to 28 and yet they are not significant. Is there is
threshold of FPKM below which Cuffdiff does not consider it an
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 chard...@mrc-lmb.cam.ac.uk 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,
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
Hello,
Could you please advise me on this probably naive question. When I compare
sample A and sample B by Ciffdiff and then separately compare Sample A to
Sample C by Cuffdiff too, should the FMPK value be the same for A in both
tests? At the moment mine does not seem to be!
Best wishes
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
Hello,
The transcript name when using RefSeq as a reference annotation is the
NM_ type of identifier.
If you want to include a gene symbol, then the reference annotation
should include the attribute gene_name. The iGenomes GTF files are an
example of datasets that include this attribute.
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
Dear Galaxy Staff:
I was wondering which version of Cuffdiff is currently running on Galaxy.
The wrapper version is 0.0.6, but I did not see the actual version of the
underlying software under the Tool Version field (please see attached
screen grab).
Thanks for your help,
Cory Dunn
[image:
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
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
Hi,
I am wondering why Cuffdiff suddenly gives many more significant DE genes?
I have used same input data and now get approx 5x more significant genes,
settings is same with the exception that you now included library normalization
and dispersion estimation. See below for parameters.
I have
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
I'm trying to run Cuffdiff on a set of 10 human samples with biological
replication then download the results for further analyses in
Cummerbund(v2.1.1). It seems like a standard workflow but I cannot get
cummerbund to acknowledge replicates. I download and rename the 11 cuffdiff
output
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,
I'll preface my concern by saying that I'm a novice to Cufflinks. Back in
September, I performed a Cuffdiff analysis comparing a wild-type and mutant
condition. The analysis returned ~800 transcripts differentially regulated
between the two with statistical significance. Recently, I've
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 jes...@case.edu wrote:
Hi,
I'll preface my concern by saying that I'm a
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
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
Hi, Galaxy user.
I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to
check differential expressed genes in my samples.
I have 3 normals and 6 cancers samples, I did the following:
- After tophat for each samples, run cufflink with refseq annotation which
has 25266 genes and
Hello guys,
I went through the RNAseq workflow (I didn't do Cuffmerge) and from the
Cuffdiff output gene and transcript differential expression testing I filtered
some data. For example, for two samples I got about 400 gene and 900 transcript
differential expressed with fold change 2. Since I
Hi,
I got confused while trying to perform Cuffdiff for my RNA sequencing analysis.
So I have five different samples which were sequenced. I used tophat to create
the bam files and cufflink to create the assembled trancripts. Then I uded
Cuffmerge to merge them in one file and then I wanted to
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
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:
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
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 that
Hello forum,
I have ran cuffdiff with two samples, treated vs untreated, and had
certain values as expressed in the output (isoform differential
expression).
When I ran it again, using a different treated sample, but SAME
UNTREATED SAMPLE, the values assigned to the untreated are different.
Why
On Wed, Oct 3, 2012 at 9:11 PM, i b ibse...@gmail.com 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
On Wed, Oct 3, 2012 at 7:35 AM, Ross ross.laza...@gmail.com wrote:
On Wed, Oct 3, 2012 at 9:11 PM, i b ibse...@gmail.com 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?
On 8/21/12 4:33 AM, i b wrote:
Thanks Jen,
useful link. But I did not understand one thing.
I have the following FPKM in cufflinks for two samples:
s1 (untreated): 1234106
s2 (treated): 159713
cuffdiff of the two samples gives me the following values:
value_1:5.4
value_2:20.9
and it is
Hello,
I am having a problem running Cuffdiff on some RNA-seq data. I want to
compare 2 samples (A and B). I did Cufflinks and Cuffmerge before running
Cuffdiff. I ran Cuffdiff with the following options: Cuffmerge + Bowtie A, B
(sorted required by Cufflinks after mapped with Bowtie). But I
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
Dear all,
I ran Cuffdiff with 3 groups: A, B, C each with 2, 5 and 1 replicates
respectively.
When looking at the transcripts dif.exp.testing, I have only sample A
and B and redpective values.
What happened to sample C?
Thanks for any help.
ib
Dear all,
has anything like this happened to you?
I compared two samples with cuffdiff and when I look at the
differentially expressed genes values I have the same gene listed for
5 times with different values.
E.g.
sample1sample2gene
71.6837 9.76435 NM_005514
87.6456
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:
Attribute
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 at
Hi,
I ran cuffdiff using Refseq genes as GTF and two groups of BAM. Group
one has two replicates (treated) and group two only one replicate
(untreated).
When looking at the outputs the following are empty (1 line):
TSS group FPKM tracking
TSS groups differential expression testing
CDS FPKM
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
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
2.what to use as input: cufflinks, cuffcompare or cuffmerge?
Thanks a lot!
___
The Galaxy
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
Dear All
I have simple and question for cuffdiff
should we run cuffdif on merge transcript file (produced by cuffmerge) and
concatenate data sets
or directly on cufflink produced files, in the later case, i have two
transcript files resulting from cufflink on sample 1 and 2 respectively,
result
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.
Dear galaxy user
After running cuffdiff on my two samples (SAM files from bowtie)
i got a list with p and q values, and löast colum is saying abou significance
with P value, it seems like the comparison should be significant, but in Q
value is 1, and last coumn is saying not significant
any one
Hello
I am having a problem running Cuffdiff on some RNA-seq data. I want to
compare 2 of my conditions. I successfully used Cuffdiff three days ago to
compare two sets of data that are processed the exact same way (align with
Tophat and use Picard to confirm adequate alignment). I am using
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
Hello!
I have an RNA-Seq project which consists of 5 samples from the
species tree shrew. When uploading these fastq files into Galaxy, I chose
unspecified (?) for the database/build since the latest tree shrew version is
not in the drop down list. When using TopHat,
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 about using an unspecified (?)
database/build
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
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
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:0-1657112484.2
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