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Hi how can I specify a GTF gene annotation file when running tophat to
guide the alignment to human genome? What is the best way to visualize
the tophat results in the context of annotated human genome, i.e.
RefSeq?
Thanks,
tao
===> Please use "Reply All" when responding to this email! <===
Hello Tao,
Sorry for the delayed reply, your question did not post to the mailing
list since the "to" was not _only_ to galaxy-user.
Going forward, please leave off any "to" or "cc" to team members when
asking a question. Send all questions directly "to"
"galaxy-user@bx.psu.edu" and do not include any "Re" or "Fwd" text in
the subject line.
Regarding RNA-seq analysis and reference GTF files, the place to
incorporate the GTF file is in the Cufflinks step, the option to
select
the GTF file from your history is on the tool's form. If you have
questions about the tools that are not addressed by these help links:
http://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faqhttp://usegalaxy.org/u/jeremy/p/galaxy-rna-seq-analysis-exercise
then contacting the tool authors would be the next step:
email tophat.cufflinks@gmail.com
To visualize the data, the available options will be links associated
with each dataset (expand the dataset box to locate these). The Galaxy
Track Browser (GTB) aka "Trackster", UCSC Genome Browser, Ensembl, and
GeneTrack are potential options; the datatype will determine which
links
are provided.
Hopefully this helps,
Best,
Jen
Galaxy team
Subject: run tophat in galaxy
Date: Sun, 28 Aug 2011 08:50:04 -0700
To: Jennifer Jackson <jen@bx.psu.edu>, galaxy-user
<galaxy-user@lists.bx.psu.edu>
Hi how can I specify a GTF gene annotation file when running tophat to
guide the alignment to human genome? What is the best way to visualize
the tophat results in the context of annotated human genome, i.e.
RefSeq?
Thanks,
tao
===> Please use "Reply All" when responding to this email! <===
Hi Tao,
I made an error in my prior reply, it is possible to guide assembly in
TopHat. To do this, on the TopHat form, change "TopHat settings to
use:"
from "Use Defaults" to "Full parameter list". In the expanded form:
1 - change "Use Own Junctions:" to be "yes".
2 - change "Use Gene Annotation Model:" to be "yes"
3 - in the new pull-down menu, select the GTF file from your history
Great question! Glad that we were able to provide you with the correct
instruction,
Best,
Jen
Galaxy team
--
Jennifer Jackson
http://usegalaxy.orghttp://galaxyproject.org/Support
Hi when I am done with cuffdiff analysis in GALAXY, I got many tabular
data output for gene, transcript, promoter and CDS differential
expression testing, I wonder if there are some systematic ways to look
at the data output from cuffdiff analysis?
Thanks,
tao
ADD REPLY
• link
written
7.2 years ago by
Peng, Tao • 170
I wrote a python script and am in the process of writing the xml
interface
to do just this at this very moment but it uses matplotlib to draw the
images. I would be happy to share it with you, but it probably would
not
work on the public site unless they have matplotlib installed or would
be
willing to install it.
The result is attached and the "error" bars are the 95% confid
intervals.
File type can be pdf or png (or pretty much anything with small code
change).
Gus
--
In science, "fact" can only mean "confirmed to such a degree that it
would
be perverse to withhold provisional assent." I suppose that apples
might
start to rise tomorrow, but the possibility does not merit equal time
in
physics classrooms.
*-Stephen Jay Gould*
Jen, thank you for following up on my question.
Is any tool in GALAXY to visualize the coverage of aligned reads from
TopHat on human chromosomes (histogram or density plot)?
Tao
To: galaxy-user
Cc: Peng, Tao
Subject: Re: [galaxy-user] run tophat in galaxy
===> Please use "Reply All" when responding to this email! <===
Hi Tao,
I made an error in my prior reply, it is possible to guide assembly in
TopHat. To do this, on the TopHat form, change "TopHat settings to
use:"
from "Use Defaults" to "Full parameter list". In the expanded form:
1 - change "Use Own Junctions:" to be "yes".
2 - change "Use Gene Annotation Model:" to be "yes"
3 - in the new pull-down menu, select the GTF file from your history
Great question! Glad that we were able to provide you with the correct
instruction,
Best,
Jen
Galaxy team
select
links
RefSeq?
--
Jennifer Jackson
http://usegalaxy.orghttp://galaxyproject.org/Support
ADD REPLY
• link
written
7.2 years ago by
Peng, Tao • 170
I have related question If I have to use Ensembl mouse GTF file
(Mus_musculus.NCBIM37.64) Do I have to download and reformat it or
Galaxy
can take it from the source directly?
Thanks
Hi Tao,
Yes, the resulting SAM dataset can be converted to BAM and viewed in
the
GTB (Galaxy Track Browser).
http://galaxyproject.org/wiki/Learn -> scroll to "Visualization" to
find:
http://galaxyproject.org/wiki/Learn/Visualization
The GTB can be reached through a different links, but one quick way to
do this is:
1 - start with TopHat's output SAM dataset
2 - use the tool "NGS: SAM Tools -> SAM-to-BAM"
3 - hover over "Visualization" in the top menu bar then click on "New
Track Browser"
4 - at the prompt, name the visualization and specify the reference
genome and click on "Continue"
5 - once the browser opens, click on the "Add Datasets to
Visualization"
prompt to add datasets. Histories and Libraries can be navigated,
selected, then individual datasets selected and loaded.
6 - default view for BAM datasets a coverage histogram.
7 - adding more tracks and other functions can be performed by using
the
left menu "Actions" on the GTB interface. Be sure to use "Save" before
navigating away if you want to use the same browser again.
If datasets are not available to add to a browser, then likely there
is
a mismatch between the browser's reference database and the database
assigned to the dataset. In some cases this can and should be adjusted
(perhaps database was unassigned after an analysis).
The SAM file can also be converted to interval, then BED format for
visualization, but BAM is the most direct route and preserves the
sequence content when zoomed in at the base level.
Hopefully this helps you and others to learn more about the GTB. This
tool is under active development. Screencasts and more example
documentation is on the way soon to offer more help.
Best,
Jen
Galaxy team
--
Jennifer Jackson
http://usegalaxy.orghttp://galaxyproject.org/Support
Thanks a lot.
Please see the attached screen shot from using Browser in GALAXY for
viewing results of Tophat. What do those numbers mean? Is there any
way
to adjust Y-axis to have the bar taller so it will be easier to see?
Thanks,
tao
To: Peng, Tao
Cc: galaxy-user
Subject: Re: [galaxy-user] run tophat in galaxy
Hi Tao,
Yes, the resulting SAM dataset can be converted to BAM and viewed in
the
GTB (Galaxy Track Browser).
http://galaxyproject.org/wiki/Learn -> scroll to "Visualization" to
find:
http://galaxyproject.org/wiki/Learn/Visualization
The GTB can be reached through a different links, but one quick way to
do this is:
1 - start with TopHat's output SAM dataset
2 - use the tool "NGS: SAM Tools -> SAM-to-BAM"
3 - hover over "Visualization" in the top menu bar then click on "New
Track Browser"
4 - at the prompt, name the visualization and specify the reference
genome and click on "Continue"
5 - once the browser opens, click on the "Add Datasets to
Visualization"
prompt to add datasets. Histories and Libraries can be navigated,
selected, then individual datasets selected and loaded.
6 - default view for BAM datasets a coverage histogram.
7 - adding more tracks and other functions can be performed by using
the
left menu "Actions" on the GTB interface. Be sure to use "Save" before
navigating away if you want to use the same browser again.
If datasets are not available to add to a browser, then likely there
is
a mismatch between the browser's reference database and the database
assigned to the dataset. In some cases this can and should be adjusted
(perhaps database was unassigned after an analysis).
The SAM file can also be converted to interval, then BED format for
visualization, but BAM is the most direct route and preserves the
sequence content when zoomed in at the base level.
Hopefully this helps you and others to learn more about the GTB. This
tool is under active development. Screencasts and more example
documentation is on the way soon to offer more help.
Best,
Jen
Galaxy team
use:"
mailing
Galaxy
and
to
visualize
--
Jennifer Jackson
http://usegalaxy.orghttp://galaxyproject.org/Support
ADD REPLY
• link
written
7.2 years ago by
Peng, Tao • 170
Hi I wonder how I can quantitatively visualize expression of a
gene/transcript which has a significant p-value/q value from splicing
differential testing from Cuffdiff analysis? I tried track browser in
GALAXY and UCSC genome browser and none of them really provide a
quantitative analysis of gene/transcript expression from Cuffdiff
results.
Thanks,
tao
To: 'Jennifer Jackson'
Cc: galaxy-user
Subject: RE: [galaxy-user] run tophat in galaxy
Thanks a lot.
Please see the attached screen shot from using Browser in GALAXY for
viewing results of Tophat. What do those numbers mean? Is there any
way
to adjust Y-axis to have the bar taller so it will be easier to see?
Thanks,
tao
To: Peng, Tao
Cc: galaxy-user
Subject: Re: [galaxy-user] run tophat in galaxy
Hi Tao,
Yes, the resulting SAM dataset can be converted to BAM and viewed in
the
GTB (Galaxy Track Browser).
http://galaxyproject.org/wiki/Learn -> scroll to "Visualization" to
find:
http://galaxyproject.org/wiki/Learn/Visualization
The GTB can be reached through a different links, but one quick way to
do this is:
1 - start with TopHat's output SAM dataset
2 - use the tool "NGS: SAM Tools -> SAM-to-BAM"
3 - hover over "Visualization" in the top menu bar then click on "New
Track Browser"
4 - at the prompt, name the visualization and specify the reference
genome and click on "Continue"
5 - once the browser opens, click on the "Add Datasets to
Visualization"
prompt to add datasets. Histories and Libraries can be navigated,
selected, then individual datasets selected and loaded.
6 - default view for BAM datasets a coverage histogram.
7 - adding more tracks and other functions can be performed by using
the
left menu "Actions" on the GTB interface. Be sure to use "Save" before
navigating away if you want to use the same browser again.
If datasets are not available to add to a browser, then likely there
is
a mismatch between the browser's reference database and the database
assigned to the dataset. In some cases this can and should be adjusted
(perhaps database was unassigned after an analysis).
The SAM file can also be converted to interval, then BED format for
visualization, but BAM is the most direct route and preserves the
sequence content when zoomed in at the base level.
Hopefully this helps you and others to learn more about the GTB. This
tool is under active development. Screencasts and more example
documentation is on the way soon to offer more help.
Best,
Jen
Galaxy team
use:"
mailing
Galaxy
and
to
visualize
--
Jennifer Jackson
http://usegalaxy.orghttp://galaxyproject.org/Support
ADD COMMENT
• link
written
7.2 years ago by
Peng, Tao • 170
Tao,
Cuffdiff output is tabular data, and hence any statistical tool that
supports tabular data can be used to analyze/visualize Cuffdiff
outputs. In Galaxy, using tools in the categories Statistics and
Graph/Display Data should enable you to visualize basic aspects of
your data.
Good luck,
J.
