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.santagostino@unipv.it

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