On Mon, Apr 23, 2012 at 11:41 PM, Sarah Hicks wrote:
> Peter, you requested an example, here are the first five hits for my
> first query sequence (OTU#0)
>
> 0 324034994 527 93.23 266 13 5 1 265
> 22 283 7e-102 379.0
> 0 56181650
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
r
So, Jen, I'm not sure if we're talking about the same ID change... I
am under the impression that GenBank does not change it's GI numbers
for it's entries. Plus, it's now looking like all sequence length
output info for each hit through Galaxy's megablast does not match to
the GI number output give
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 w
Thanks for the update! I am not in a huge rush, but I was worried I
had not been describing the problem clearly, as it took quite a while
to explain to colleagues here :)
best
On Tue, Apr 24, 2012 at 3:24 PM, Jennifer Jackson wrote:
> Hi Sarah,
>
> We appreciate all of the information you have pr
On Tue, Apr 24, 2012 at 10:24 PM, Jennifer Jackson 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 obtained f
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
http://uswest.e
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
Ok, I'll work on installing this...
On Tue, Apr 24, 2012 at 4:08 PM, Jennifer Jackson wrote:
> 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
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 A
10 matches
Mail list logo
