FYI: samtools + bam file + a bit of perl == to wiggle conversion:
https://lists.soe.ucsc.edu/pipermail/genome/2010-December/024318.html
- Original Message -
From: Ying Zhang ying.zhang.yz...@yale.edu
To: galaxy-u...@bx.psu.edu
Sent: Monday, February 21, 2011 12:39:47 PM
Subject:
Listed on the hg19 gateway page at the UCSC genome browser.
- Original Message -
From: David Matthews d.a.matth...@bristol.ac.uk
To: Jennifer Jackson j...@bx.psu.edu
Cc: galaxy-u...@bx.psu.edu
Sent: Monday, March 28, 2011 2:04:02 PM
Subject: Re: [galaxy-user] Pseudo Autosomal regions in
Good Morning Dr. Hunt:
Can you please clarify what upload function from galaxy you are
trying to perform ? Perhaps the galaxy user help email list
could direct you to advice on this subject ? (copied on this
email) The Ensembl genome browser accepts the same types of
upload tracks as does the
FYI: The bedToBigBed converter is one of the lower memory
usage big* converters, with a longer running time:
http://genomewiki.ucsc.edu/index.php/Big_file_converters
--Hiram
___
The Galaxy User list should be used for the discussion of
There are at least six of them there. Which one ?
- Original Message -
From: Noa Sher noa.s...@gmail.com
To: Hiram Clawson hi...@soe.ucsc.edu
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my previous mail
Is this the genome you are working with:
http://archaea.ucsc.edu/cgi-bin/hgGateway?db=procMari_CCMP1375
- Original Message -
From: Noa Sher noa.s...@gmail.com
To: Hiram Clawson hi...@soe.ucsc.edu
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re
with the format.
I can't see immediately how to use it properly.
--Hiram
- Original Message -
From: Noa Sher noa.s...@gmail.com
To: Hiram Clawson hi...@soe.ucsc.edu
Cc: galaxy-user@lists.bx.psu.edu
Sent: Sunday, December 4, 2011 11:10:06 AM
Subject: Re: [galaxy-user] there was a wrong link in my
Good Afternoon Sheena:
Can you please explain what is different between the Ensembl and UCSC
Zebrafish Zv9 genome sequences ?
--Hiram
On 11/4/11 2:50 PM, Scroggins, Sheena wrote:
How do I upload the Zebrafish genome from Ensembl to my user history
in Galaxy? I'm trying to map my RNA-Seq data
Good Evening Jose:
Please note the types of graphing formats you can display at UCSC:
http://genomewiki.ucsc.edu/index.php/Selecting_a_graphing_track_data_format
I would recommend converting your bedgraph file to a bigWig file and display
that via a remote URL. This would be your most
Please note the arguments you can use in a track line
for a type=wiggle_0 format file:
http://genome.ucsc.edu/goldenPath/help/wiggle.html
The arguments useScore, scoreMin, scoreMax have no meaning
with a wiggle track. A wiggle track does not display items
in a gray-scale fashion, it draws a
I'm curious what is this genome called 'hg_g1k_v37'
and how does it correspond to NCBI GRCh37 which is
identical to UCSC hg19 ?
--Hiram
Jennifer Jackson wrote:
UCSC does not contain the genome 'hg_g1k_v37' - the genome available
from UCSC is 'hg19'.
Even though these are technically the
Good Morning Galaxy Universe:
What is the data expiration policy at Galaxy for user created
big* files that are then subsequently used in custom tracks
at UCSC ? We are noticing users with bigDataUrl paths of:
https://main.g2.bx.psu.edu/display_application/.../somefile.bigwig
which appear to
Please note, this sequence chrM_rCRS does not exist in the human/hg19
genome browser at UCSC. It is not a recognized sequence.
There is a note about this on the gateway page:
http://genome.ucsc.edu/cgi-bin/hgGateway?db=hg19
See the paragraph titled: Note on chrM
--Hiram
On 9/12/13 1:25 AM,
13 matches
Mail list logo
