Hi all,
can anyone explain me wh how can I visualize cufflinks outputs in trackster?
galaxy keep sending me errors
thanks,
ib
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Hello forum,
I was reading some of the theory behind cuffdiff and how it calculates
for DE genes.
My question:
if I do not have replicates, how does cuffdiff do the test statistic
which is dependent on the variance?
The manual says "Note that in order to calculate the test statistic T,
we need to
Dear forum,
whoever knows this please tell me!
Given two fpkm . e.g. fpkm 1=2922828 and fpkm 2=0, why cuffdiff does
not calculate differential expression. those genes are listed in
cuffdiff as not significant and the log2 fold change is infinite ,
either negative or positve...how do i conside
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 i
Hi,
I am trying to open the "i" icon on galaxy to look at the information
of each job, but this does not opne for old jobs, only the last recent
one ...
Any suggestion?
Thanks,
ib
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dear all these are the cuffdiff outputs for the same transcript/gene
(one isoform only):
transcript differential expression
value1 value2log2fold test stat pvalue
q value significant
18.8175 114.371 2.60357 -2.883580.00393177 0.0630024 no
dear all,
how can we use the tophat deletions output?
e.g. if I want to see and conpare between two samples if a specific
gene or transcript had been deleted, how can I use this output?
is visualisation enough?
thanks,
ib
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Dear all,
I have two samples, treated and untreated.
I ran cufflinks and had the following FPKM:
treated: 884532
untreat.: 130247
I then ran cuffdiff and look at the transcript diff. expression values:
treated: 33
untreat.:2.9
significant:yes
Strangely for another transcripts I have the followi
Dear all,
I have two samples, treated and untreated.
I ran cufflinks and had the following:
treated: 884532
untreat.: 130247
I then ran cuffdiff and look ath transcript diff. expression:
treated: 33
untreat.:2.9
significant:yes
Strangely for another transcripts I have:
Cufflinks: treat_:0
Dear all,
in cuffdiff outputs e.g. transcript differential expression, I find for example:
value_1 value_2 log2(fold_change)
7.77183 0 -1.79769e+308
or
value_1 value_2 log2(fold_change)
0 14.5972 1.79769e+308
for many many rows.
if I sort in excel my data by fold change column (big
Hi,
I have used for the first time this tool, picard bam statistic.
I have aligned my reads to a custom genome (7904 bp long) and had the
following output:
length= 7904 Aligned= 44 Unaligned= 0
Why is unaligned =0.
I had the unaligned =0 also when aligning agaist hg19...
thanks,
ib
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
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
_
Hi all,
what is the difference between using "NGS:mapping---Map with
Bowtie for Illumina" and "NGS: RNA analysis-Tophat for
Illumina" when mapping reads against a reference/custom genome?
thanks,
ib
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Dear all,
I managed to upload to Galaxy a genome of interest in .fasta format
from NCIB website.
However, Galaxy does not recognize it as input to run Tophat...
Wht format has to be to be used as referece genome for tophat?and how
can i convert it?
Any suggestion?
thanks,
ib
___
Dear all,
given 3 samples, 1 control and 2 treated replicates when I do
cuffcompare to produce the gtf input for cuffdiff, do I have to run it
with or without the cufflink control?
E.g. Cuffcompare with only my 2 treated replicates?--use
this gtf to run cuffdiff
Cuffcompare 1 con
hi,
I would like to upload the HPV16 W12E genome (AF125673) (human
papilloma virus type 16 ) but I find it hard to be accepted by galaxy.
Any suggestion where I can find the correct one?
thanks,
ib
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Hi guys,
have a question about the cuffdiff output "differential expression testing".
For most of you might sound "naive" but I'm new to this field and I
have very little background in statistic.
So, I have compared a control sample with 2 biological replicates
using cuffdiff. I have now about 40
Hi guys,
a bit of confusion about how to give cuffdiff certain outputs:
having 1 control and 8 tumour samples which I consider biological
replicates (not technical replicates), how shall give the input to
cuffdiff?
If I want to use cuffcompare as gtf: shall I cuffcompare all 8samples
plus the cont
Hi,
I am a bit confused about two outputs of cuffdiff:
If I want to see if two samples, e.g. treated and un-treated express
similar protein levels, what would be best to look at gene
differential expression or transcript diff. expression?
Thanks,
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 27.3
Hello,
if I am looking for DE between samples and ran cufflinks without
reference annotation, does it mean that when I ran cuffcompare and
cuffmerge I DOTN'T HAVE to select a refence annotation in the options?
Also,how are my cufflinks fected wheter i use the reference annotation
or not?In galaxy
ok, im really confused now about cufflinks and its tools.
All I wanted was to look for differentially expressed genes between
two samples: treated (2 replicates) and control (one replicate).
can anyone give me a workflow for a similar analysis with the various
options chosen?
I have read a lot o
Hi,
I had 3 samples (2replicates treated (A-B) and one untreated (C) ).
I did cufflnks and cuffmerge (all 3 cufflinks)
I run cuffdiff with the following options:
cuffmerge
+ tophats from A, B, C (2 groups: gr.one with A, B), gropu2: C.
I had the following message:
0 bytes
An error occurred run
Hi,
where can I find an explanation of the columns in the splice junctions
output? From 7 to12 they are only numbered
thanks,
ib
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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 tracki
Hi,
is there a way to create a jobin my history from UCSC genome browser
that contains ONLY genes encoding for ONLY cell surface proteins?
How can I do that?
Thanks a lot!
ngs-ib
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G
Hi,
I ran cuffcompare using 3 samples as inputs (dataset 1-2-3 cufflinks
gtf) and a reference annotation (dataset 4).
These are the outputs:
5: Cuffcompare on data 1, data 4, and others: transcript accuracy
6: Cuffcompare on data 1, data 4, and others: 1 data tmap file
7: Cuffcompare on data 1, da
ok, so if I have 3 different samples I would use 3 different goups and add
my samples as replicate within each group.
or did you mean to create just one group and add all my 3 samples as 3
replicates within that only group?
thanks a lot
ngs-ib
From: Jenni
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