Hi, JiWen
I thought about this before, here is the answer from Cole Trapnell from
Seqanswer website:
I can shed some light on this. We have an upcoming protocol paper that
describes our recommended workflow for TopHat and Cufflinks that discusses
some of these issues.
As turnersd outlined,
Hi Greg,
Upload your files to a Galaxy data library using a combination of Upload files
from filesystem paths without copying data into Galaxy's default data store.
See the following wiki for all the details:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
For all
I am having trouble finding information on the MegaBLAST output
columns. What is each column for? I can't seem to figure this out by
comparing info in the columns to NCBI directly because the GI#'s don't
match with the correct entry on NCBI. I've seen that others have
posted about that problem, so
Thank you very much for your help with this - we got that settled. One
other question...we are importing sorted, indexed bam files into a galaxy
data library and we are not having galaxy copy over the files (they are
large) but rather just setting up galaxy such that it points to the
relevant
Hi Greg,
Even though you are not copying the data into Galaxy's default data store,
Galaxy determines and stores certain metadata for each of the data files to
which you are linking. One of the types of metadata defined for the Bam
datatypes is it's index, which is created by a call to
Hi Sarah,
Peter defined the columns (thanks) but I can provide some information
about the GenBank identifiers. The megablast database on the public
server are roughly a year old and there have been updates at NCBI since
that time. As I understand it, this manifests as occasional mismatches
Thanks again for the feedback...one final (hopefully) thingas I
mentioned in first e-mail, we are trying to add a large (~170 GB) BAM
file to a library with just a link to the file (no copying). After at
least an hour of working, I get the error message Unable to finish
job,
tool error. Any
Is there something helpful in your paster log about the cause?
On Apr 23, 2012, at 4:34 PM, Gregory Miles wrote:
Thanks again for the feedback...one final (hopefully) thingas I
mentioned in first e-mail, we are trying to add a large (~170 GB) BAM
file to a library with just a link to the
Thanks so much for the prompt reply. I don't mind using last years
GenBank, as long as I am getting accurate hits. I just have a couple
more questions to confirm I am safe using the Galaxy pipline for
this...
So if I continue to work within the the 1 year old database, can I
trust the output as
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 56181650513 93.26 267 10 8 1 265
25
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