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 any
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 yo
> 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 whi
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 r
> 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 bu
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 dif
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 Medicine
Arthur,
When the data is coming from casavA 1.8 (actually I believe from 1.5 and above)
I think it's already in the proper format.
An excellent overview is here: http://en.wikipedia.org/wiki/FASTQ_format
Basically the headers of the fastq reads are my indication at the moment. Since
1.8 it change
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