Blast2GO local instance Re: Table with gene count reads - galaxy-user

23 Mar 2012

      Howdy,
   Thanks Jen, I will try it tomorrow.
I installed Blast2Go from the Toolshed in my local instance of Galaxy
and when I try to run it I get the following error:
Index file named 'blast2go.loc' is required by tool but not available.
I logged as admin and the installation did not gave me any error. From
the terminal:
galaxy.util.shed_util DEBUG 2012-03-23 17:23:37,088 Installing repository
'blast2go'
galaxy.util.shed_util DEBUG 2012-03-23 17:23:37,088 Cloning
http://testtoolshed.g2.bx.psu.edu/repos/peterjc/blast2go
destination directory: blast2go
requesting all changes
adding changesets
adding manifests
adding file changes
added 2 changesets with 6 changes to 3 files
updating to branch default
3 files updated, 0 files merged, 0 files removed, 0 files unresolved
galaxy.util.shed_util DEBUG 2012-03-23 17:23:42,798 Updating cloned
repository to revision "7b53cc52e7ed"
Anyway, I was thinking to use it because most of my differentially
expressed genes are unknown. I was thinking to use Blast2GO to get them at
least clustered in functional groups. I am not sure if that would be the
best approach to find what might be the function of these genes. I also
checked the list of public services that might have this tool, and Berkeley
BOP is listed, but it seems that they no longer have the server or it was
down when I checked (or the link is broken http://galaxy.berkeleybop.org/).
Thank you.
Luciano
On Fri, Mar 23, 2012 at 8:43 AM, Jennifer Jackson jen@bx.psu.edu wrote:
...
Hello Luciano,
There is no single tool do to this operation (although there has been some
discussion about including one in the Tool Shed), but the same information
can be obtained by using a combination of existing tools.
First, start by converting both starting datasets to interval format.
mapped reads:

for TopHat output, "NGS: SAM Tools -> Convert SAM to interval"

features:

for GFF file (convert to tabular if necessary), subtract "1"
from the start position's value using tool "Text Manipulation ->
Compute"
cut columns chrom, new start, stop, strand, name, and score from
this result file using "Text Manipulation -> Cut"
set the data type to "interval" using the 'Edit attributes form
(pencil icon)

Next, use a tool in the group "Operate on Genomic Intervals" to compare
these intervals for overlap. The tool "Cluster" with the option "Find" is
mostly likely the one you will want to use.
As a final step, summarize the data by feature using the tool "Join,
Subtract and Group -> Group".
Hopefully this helps,
Best,
Jen
Galaxy team
On 3/19/12 4:36 PM, Luciano Cosme wrote:
...
Hi,
   I was wondering if there is any tool on Galaxy were I can obtain a
table with how many reads have been mapped to a given sample and to a
given gene (for example, use a Tophat output and use a GFF file to
obtain the table). I am using HTSeq to get it (htseq-count). There is
also GenomicRanges and easyRNASeq packages in bioconductor.
Thank you.
Luciano
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