Hello,
I'm a galaxy newbie and running into several issues trying to adapt an
R script to be a galaxy tool.
I'm looking at the XY plotting tool for guidance
(tools/plot/xy_plot.xml), but I decided not to embed my script in XML,
but instead have it in a separate script file, that way I can still
Hi Sarah,
We appreciate all of the information you have provided and have been
working here since yesterday to investigate the issue in more detail.
This includes incorporating the additional data both you and Peter have
been posting.
We don't have anything conclusive to report yet, but it
On Tue, Apr 24, 2012 at 10:24 PM, Jennifer Jackson j...@bx.psu.edu wrote:
..., using
the BLAST+ BLASTN megablast wrapper that Peter authored, in a local or cloud
instance, would be the best immediate remedy (this version has the standard
12 column output). Sequence length data could always be
Hi Wei,
BioMart has tools to extract tabular data that maps Ensembl transcript
identifiers to alternate identifiers, gene symbols, etc. See the tool
under Get Data - BioMart Central server. You'll likely have to map
from Ensembl transcriptID - HGNC transcript - HGNC gene
Thanks Peter,
Excellent point. From there, the Cut tool could be used to reorganize
the output to exactly match that of the 13-column regular megablast
output. So, no external data needed, no tool modifications needed.
This can't be done on the main public Galaxy instance as BLAST+ is not
Hi Ateequr,
This post from today has information another member found at
seqanswers.com, directly from the CuffLinks/Merge/Diff tool author:
http://user.list.galaxyproject.org/Re-1-cuffcompare-or-cuffmerge-td4581029.html
Best,
Jen
Galaxy team
On 4/17/12 8:00 AM, Ateequr Rehman wrote:
Dear
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