Re: [galaxy-user] How to analyze the Encode RNA-seq data from UCSC genome browser with Galazy

2013-05-11 Thread Santagostino Marco 
Dear Jennifer,

thank you, I already checked the coverage with the GENCODE and found those
loci overlapping with the annotations. I also tried to overlap with the
tracks Small RNA-seq from ENCODE/Cold Spring Harbor Lab and ENCODE RNA-seq
Tracks a few of the loci not covered by GENCODE annotation.
Since some of my loci do overlap with regions that are transcribed
according to the two above-mentioned tracks, I would like to proceed with
this analysis, but the number of tables per track to be searched is big, so
I was wondering whether Galaxy would allow to make the work easier.
Here is an example the loci I am analysing,
http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr1:41965319-41965336&hub_4607_uniformRNA=full
It does not overlap with annotated Gencode transcript, but it overlaps with
"Long RNA-seq from Encode/Cold Spring Harbor Lab" ("GM78 cel pa-")  and "ENCODE
Long RNA-seq and Short RNA-seq Contigs and Signal" (GM12878 Nucleus PolyA
Long CSHL Contigs (contig_17188)), the two tracks probably refers to the
same contigs, but they use a different level of detail.

Thank you,

Marco







2013/5/9 Jennifer Jackson 

>  Hi Marco,
>
> Each RNA-seq study in the ENCODE project may have variable coverage, but
> if the goal is to identify overlapping regions with gene annotations
> targeted by the ENCODE project, the "GENCODE Genes" track is most likely
> the one you are looking for.
>
> Review the contents of the track at the ENCODE hub at UCSC by going to
> their web site http://genome.ucsc.edu, clicking into Genomes, the target
> genome (hg19?), then scroll down to the track group "Gene and Gene
> Predictions". Click on the track "Gencode genes" to read about how it is
> constructed, what the content options are, and how these relate to ENCODE
> builds. You can follow more links in the description to the subtracks (for
> example, in hg19, Version 14 is the most current), and "describe schema"
> will take you into the Table Browser where the actual format of the data
> table can be reviewed. "Tools -> Table Browser" will bring you to a form
> where the table can be extracted and sent to Galaxy, it is the same form
> found in Galaxy under "Get data -> UCSC Main".
>
> If you start this browser process while still logged into Galaxy from the
> history you want to import the data in to, you can extract directly from
> here, making sure that "Galaxy" is checked (it will be by default) next to
> the "output format: BED" section of the form. Or, you can simply explore,
> and once you know what tracks/tables you are interested in, go through the
> Galaxy tool "Get data -> UCSC Main".
>
> You may know this already, but the core hub for ENCODE is at:
> http://genome.ucsc.edu/ENCODE/index.html
>
> Basic examples that show how to extract data from UCSC and use coordinate
> overlap comparison tools can be found at:
> https://main.g2.bx.psu.edu/u/aun1/p/galaxy101
> https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 (protocol
> 1)
>
> More screencasts/tutorials are at:
> http://wiki.galaxyproject.org/Learn/Screencasts
> https://main.g2.bx.psu.edu/page/list_published
>
> Hopefully this helps,
>
> Jen
> Galaxy team
>
>
> On 5/9/13 11:01 AM, Santagostino Marco wrote:
>
> Dear Sir/Madam,
>
>  I am new at Galaxy. I need to define if a set loci ( about 700) is
> transcribed, i.e. these loci overlap with those reported in the Encode
> RNA-seq data. The track contains several tables, can you please suggest me
> how to proceed? do I need to download all the tables from UCSC table
> browser and then upload/send them to Galaxy? Is there a way to refer only
> to the Encode RNA-seq track without downloading the whole table set?
> I have the coordinates of each one of my loci, from those I can obtain the
> sequences. I intended to use the Public Galaxy Main Instance.
>
>  Thank you,
>
>  Marco Santagostino
>
>
>
>  --
> Marco Santagostino, PhD
> Laboratorio di Biologia Molecolare e Cellulare
> Dipartimento di Biologia e Biotecnologie, University of Pavia
> Ferrata street, 9 - 27100 Pavia, Italy
> Tel.: +39 0382 985540
> Fax: +39 0382 528496
> e-mail: marco.santagost...@unipv.it
>
>
> ___
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>   http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>   http://galaxyproject.org/search/mailinglists/
>
>
> --
> Jennifer Hillman-Jackson
> Galaxy Support and Traininghttp://galaxyproject.org
>
>


-- 
Marco Santagostino, PhD
Laboratorio di Biologia Molecola

Re: [galaxy-user] How to analyze the Encode RNA-seq data from UCSC genome browser with Galazy

2013-05-09 Thread Jennifer Jackson 

Hi Marco,

Each RNA-seq study in the ENCODE project may have variable coverage, but 
if the goal is to identify overlapping regions with gene annotations 
targeted by the ENCODE project, the "GENCODE Genes" track is most likely 
the one you are looking for.


Review the contents of the track at the ENCODE hub at UCSC by going to 
their web site http://genome.ucsc.edu, clicking into Genomes, the target 
genome (hg19?), then scroll down to the track group "Gene and Gene 
Predictions". Click on the track "Gencode genes" to read about how it is 
constructed, what the content options are, and how these relate to 
ENCODE builds. You can follow more links in the description to the 
subtracks (for example, in hg19, Version 14 is the most current), and 
"describe schema" will take you into the Table Browser where the actual 
format of the data table can be reviewed. "Tools -> Table Browser" will 
bring you to a form where the table can be extracted and sent to Galaxy, 
it is the same form found in Galaxy under "Get data -> UCSC Main".


If you start this browser process while still logged into Galaxy from 
the history you want to import the data in to, you can extract directly 
from here, making sure that "Galaxy" is checked (it will be by default) 
next to the "output format: BED" section of the form. Or, you can simply 
explore, and once you know what tracks/tables you are interested in, go 
through the Galaxy tool "Get data -> UCSC Main".


You may know this already, but the core hub for ENCODE is at:
http://genome.ucsc.edu/ENCODE/index.html

Basic examples that show how to extract data from UCSC and use 
coordinate overlap comparison tools can be found at:

https://main.g2.bx.psu.edu/u/aun1/p/galaxy101
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 (protocol 1)

More screencasts/tutorials are at:
http://wiki.galaxyproject.org/Learn/Screencasts
https://main.g2.bx.psu.edu/page/list_published

Hopefully this helps,

Jen
Galaxy team

On 5/9/13 11:01 AM, Santagostino Marco wrote:

Dear Sir/Madam,

I am new at Galaxy. I need to define if a set loci ( about 700) is 
transcribed, i.e. these loci overlap with those reported in the Encode 
RNA-seq data. The track contains several tables, can you please 
suggest me how to proceed? do I need to download all the tables from 
UCSC table browser and then upload/send them to Galaxy? Is there a way 
to refer only to the Encode RNA-seq track without downloading the 
whole table set?
I have the coordinates of each one of my loci, from those I can obtain 
the sequences. I intended to use the Public Galaxy Main Instance.


Thank you,

Marco Santagostino



--
Marco Santagostino, PhD
Laboratorio di Biologia Molecolare e Cellulare
Dipartimento di Biologia e Biotecnologie, University of Pavia
Ferrata street, 9 - 27100 Pavia, Italy
Tel.: +39 0382 985540
Fax: +39 0382 528496
e-mail: marco.santagost...@unipv.it 


___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

   http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

   http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/

[galaxy-user] How to analyze the Encode RNA-seq data from UCSC genome browser with Galazy

2013-05-09 Thread Santagostino Marco 
Dear Sir/Madam,

I am new at Galaxy. I need to define if a set loci ( about 700) is
transcribed, i.e. these loci overlap with those reported in the Encode
RNA-seq data. The track contains several tables, can you please suggest me
how to proceed? do I need to download all the tables from UCSC table
browser and then upload/send them to Galaxy? Is there a way to refer only
to the Encode RNA-seq track without downloading the whole table set?
I have the coordinates of each one of my loci, from those I can obtain the
sequences. I intended to use the Public Galaxy Main Instance.

Thank you,

Marco Santagostino



-- 
Marco Santagostino, PhD
Laboratorio di Biologia Molecolare e Cellulare
Dipartimento di Biologia e Biotecnologie, University of Pavia
Ferrata street, 9 - 27100 Pavia, Italy
Tel.: +39 0382 985540
Fax: +39 0382 528496
e-mail: marco.santagost...@unipv.it
___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/