Hi Loubin,
Under the toolset "Metagenomic analyses" are a suite of tools for
taxonomic analysis, including a viewer for phylogenetic relationships.
Please let us know if you would like more assistance,
Best,
Jen
Galaxy team
On 5/13/11 8:35 AM, Luobin Yang wrote:
Hi,
Do you guys know any p
Hello Bony,
First, you will need to map your data to a reference genome (either
native to Galaxy or one that you load into your history). Use the tools
under "NGS Toolbox" or map the data using your own tools and upload.
To link in MAF conservation data, use tools under "Fetch Alignments".
T
Hello Teja,
If you have a fasta file of sequences, you can map them to a reference
genome to obtain a SAM file (which you could then compress into BAM).
See the tool section "NGS Toolbox".
BLAST is an alignment tool and additional parsing/analysis tools would
be needed in order to identify S
Dear Galaxy Team,
Is there a way to download file >4Gb from the PSU Galaxy server?
I have been working with Galaxy both on the PSU server and on the cloud. I know
how to download large files (eg BAM) from the cloud by ssh into the instance,
but is there a way to get large file from the PSU se
Hello Teja,
Exploring the "Pages" tutorials is recommended as many have SNP-specific
analysis examples. I am not sure if your data is RNA or DNA or if you
have quality scores available, but there are tutorials that cover most
common-use cases.
http://main.g2.bx.psu.edu/page/list_published
I
Hello Mike,
You can fetch data from the public server using wget or curl. The link
to download can be obtained by right clicking the floppy disk icon
inside a history item and choosing "Copy Link Address." Once you have
the link:
% wget ''
or
% curl -O ''
The quotes aren't strictly nece
Hello Curtis,
The coordinates of your match are with respect to the fasta sequence,
not with respect to the reference genome. Only data mapped to the
reference genome can be viewed in the UCSC Browser
You will need to calculate from the position of the match in the fasta
sequence back throug
I have tried to follow the steps: File 33 in my history is generated by
using filter GTF data by attributes. Two files used were file 29 which is a
splicing diff file filtered for yes and file 2 is combined GTF. I used
TSS-id for filtering. the out put file file 32 is empty. Any suggestion?
Jaga
Jennifer,
Thanks for the outline. I'll try that approach.
However, it seems rather painful to have to join the fuzznuc output back to the
original fasta to get at the header information that really should have been
passed along. It would see that there must be a way to get the data out of UCS
9 matches
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