Hi,
This may be a dense question, but how do we generate a vcf file from the public
version of Galaxy? Am I missing something obvious?
Best Wishes,
David.
__
Dr David A. Matthews
Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular
Dear All,
I have been successful by using the online tool to align Illumina pair end
reads , each direction 5GB, and also generated a pileup of 680,000,000
lines,
but the filtering of the pileup always fails, it runs for several hours and
I get an empty file back. I tried different options and
The problem ended being the use of Perform Bias Correction(-b) and a
GTF file with no Database/Build associated. Looking at cuffdiff
wrapper I found, if a FASTA reference is not selected from the
history, the FASTA reference of the GTF file associated build is used.
If there is not build
Dear Sir or Madam,
I am planning to do clustering of several libraries based on the output of
cuffcompare or cuffdiff, as they allow me to construct a matrix whose columns
represent the libraries and rows are the count of transcripts or genes. I want
to construct the matrix because it is the
1. It seems that it is better to run everything up to cuffdiff, but does
cuffdiff allow multiple sample comparison because I read somewhere that even
for multi-samples it still compare tham pairwisely?
Cuffdiff supports replicate analysis.
In a sense, because I want to do clustering which
Hello Sebahattin,
It may be that the data is too large to run on the Galaxy public
instance, which means that a local or cloud instance would be the next
recommendation, as explained in this wiki:
http://wiki.g2.bx.psu.edu/Big%20Picture/Choices
But, before you make the investment of moving
Hi Philipp,
Sorry for the delay in reply, the question is a bit confusing since the
conversion tools allow for the adapter base to be specified (and the
default is a G). I am not sure we are talking about the same tool, so to
clear things up, would you please send a shared history link and
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