I want to extract TSS ids with correspodning location for Hg19. Once I
extract such TSS coordinates I want to have there annotation either with
enetrz gene id or some other unique Ids. I am sure Galaxy can do this, But I
dont know where to start, or which workflow to use. Can some one please
dirce
Le 02/06/2011 21:39, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
default_cluster_job_runner will remain for backwards compatibility, but
we'll ship a sample job_conf.xml that runs everything locally by
default.
--nate
Haha, and I did that before realizing I could do just what I needed b
Louise-Amélie Schmitt wrote:
> Le 02/06/2011 21:39, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>>default_cluster_job_runner will remain for backwards compatibility, but
> >>>we'll ship a sample job_conf.xml that runs everything locally by
> >>>default.
> >>>
> >>>--nate
> >>Haha, and
Le 06/04/2011 13:57, Nate Coraor a écrit :
Louise-Amélie Schmitt wrote:
Hello everyone
I observed an issue when flagstat is incorporated in a workflow in which
the BAM file it works on is also used by another program (generate
pileup for instance) and is NOT the input dataset (generated by sam
Louise-Amélie Schmitt wrote:
> Le 06/04/2011 13:57, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>Hello everyone
> >>
> >>I observed an issue when flagstat is incorporated in a workflow in which
> >>the BAM file it works on is also used by another program (generate
> >>pileup for instan
Hello,
One direct method is to import data using "Get Data -> BioMart".
Choose "ENSEMBL GENES 62", then "Homo sapiens genes (GRCh37.p3)". In the
left side bar, click on "Attributes". In the resulting form, select
"Structures", then open GENE and check "Transcript Start" and
"Associated Gene N
Hi guys,
We are trying to load Illumina data to our local Galaxy instance. The
files are between 700 MB and 2.2 GB. Files below 2 GB load in less than
5 minutes. Files larger than 2 GB don't upload at all. We installed
Galaxy locally because we thought loading files will be faster than the
se
Short update:
I forgot to mention that you will probably want to include the
chromosome and strand under the "GENE" options.
Also, do not select "Associated Gene DB" during the export (just examine
this at BioMart to note the source) as this will output some html
content not allowed in a Gal
Jennifer,
Thanks for your help so far.
I've been trying to implement the approach you outlined. It seems to be taking
a lot of steps. I think I'm now at the last step, where I convert my TAB format
file into a BED and push it to USCS for viewing. But I don't see anything that
will allow me t
Hi Curtis,
Two more steps were needed, I ran them in this history:
http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/h/re-galaxy-user-ucsc-embossfuzznuc-ucsc-workflow-63
1 - removed the first column ("hg19") from dataset #38, using the "Text
Manipulation -> Cut" tool
2 - in the resulting dataset
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