dear all,
how can we use the tophat deletions output?
e.g. if I want to see and conpare between two samples if a specific
gene or transcript had been deleted, how can I use this output?
is visualisation enough?
thanks,
ib
___
The Galaxy User
Hi,
I am trying to upload new files to galaxy via FTP using Filezilla.
I have this error message:
530 Sorry, the maximum number of clients (3) for this user are already
connected.
What can I do?
Julie
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The University of Edinburgh is a charitable body, registered in
Scotland, with
On 8/21/12 4:33 AM, i b wrote:
Thanks Jen,
useful link. But I did not understand one thing.
I have the following FPKM in cufflinks for two samples:
s1 (untreated): 1234106
s2 (treated): 159713
cuffdiff of the two samples gives me the following values:
value_1:5.4
value_2:20.9
and it is
Howdy Jianguang,
There's a more complete description of the SAM format in The Sequence
Alignment/Map format and SAMtools, Li et al, Bioinformatics (2009). And
you can find the latest specification for the format at
samtools.sourceforge.net .
In the spec, the terminology for the ISIZE field has
I am developing several tools that will need to read and write multiple data
files at once. For example, Eisen Cluster produces a heatmap which consists of
three files: a .cdt file, .atr file and a gtr file which are the underlying
heatmap and the array tree and the gene tree. All three
Hi Julie,
This was mostly likely an issue on our side. Please try to FTP again and
let us know if you continue to have problems.
Our apologies for the inconvenience,
Jen
Galaxy team
On 8/21/12 3:23 AM, Julie Rodor wrote:
Hi,
I am trying to upload new files to galaxy via FTP using
Hi,
I am trying to upload 12 fastq files to Galaxy via FTP. The FTP is randomly
loosing connection, caussing interruption of the upload. Can you let me
know what is wrong?
Thanks,
fatih
___
The Galaxy User list should be used for the
Dear All,
I have run programs from Tophat to Cuffdiff of Galaxy to look for the
difference in alternative splicing events between cell types. However I do not
know how to find the detail information (such as the sequence and the genomic
coordinates) of the alternatively spliced part of a
On Tue, Aug 21, 2012 at 4:46 PM, Ted Goldstein t...@soe.ucsc.edu wrote:
I am developing several tools that will need to read and write multiple
data files at once. For example, Eisen Cluster produces a heatmap
which consists of three files: a .cdt file, .atr file and a gtr file which
are
Dear All,
I was wondering if it would be possible to add Mycobacterium
tuberculosis H37Rv as a reference genome to the list of built-in indexes
in the Map with Bowtie for Illumina (version 1.1.2) tool.
Thank you,
Sarah
___
The Galaxy User
Hi,
I've recently installed galaxy. I was trying to find how to upload
multiple files without the need to compress them into a zip/gz file first. Is
this possible? As the Get Data option allows only one file at a time. I
searched the galaxy archive mailing list but didn't find anything
Hi,
I have been having FTP issues for the past several days. I am using Filezilla.
The upload starts, then stops after about 32MB and the connection closes and
tries to reopen, then closes again. I also tried the command line ftp client
in win7 with same results.
rich
Hi,
There's this error message in my apache log:
[error] Request exceeded the limit of 10 subrequest nesting levels due to
probable confguration error. Use 'LimitInternalRecursion' to increase the
limit if necessary. Use 'LogLevel debug' to get a backtrace., referer: ...
When I turn the apache
When uploading a file using “Get Data” it seems the file is renamed to
dataset_’id’.dat in ~/database/files/000/. Is it possible for the file to keep
its name rather than being renamed?
It seems this is being done because of the line
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