Hello,
On 6/17/13 12:24 PM, Hoang, Thanh wrote:
Hi Jen,
Thank you very much for your quick response.
I have just downloaded GTF file ( Mus musculus, UCSC, mm10) from
iGenome.
Correct me if I am wrong. I should start everything from the beginning
again by uploading the GTF file to Galaxy via
Hello Thanh,
These attributes would come from the reference GTF or GFF3 file that you
are using (not the reference genome). It looks like you are not using
one, or that it did not cover this particular gene bound.
The iGenomes GTF files are preferred as they contains all of the
attributes th
Hello Hadrien,
If using a local or CloudMan Galaxy, watch the category "Metagenomics"
of the Tool Shed for potential tools. For example, right now the "
mothur_toolsuite" is one example option for this type of analysis.
http://getgalaxy.org
http://usegalaxy.org/cloud
http://toolshed.g2.bx.psu
Hi guys,
I am trying to examine gene differential expression in my mouse samples
using :
Cufflink >> Cuffmerge>>Cuffdiff
The output from Cuffdiff shows only gene id, but not gene name:
test_id gene_idgenelocussample_1
sample_2
XLOC_01XLOC_01- 1:32002
Hello Joshua,
It may be that the local instance is running out of memory and the
custom reference genome approach is the wrong one for your
configuration. Instead, try installing the reference database as a
built-in index.
Instructions are here:
http://wiki.galaxyproject.org/Admin/NGS%20Loca
Hello,
Have you seen the tool ' Get Data -> ENA SRA"?
Once a project is searched for, you will find direct links to import the
FASTQ data direct into Galaxy. Both the original submitted and the
processed archive format in many cases.
Best,
Jen
Galaxy team
On 6/16/13 7:54 AM, Murphy, There
Is it possible to upload files from the NCBI sra data base, then use fastq-dump
from the sra toolit within galaxy? If not, could these tools be added?
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