Dear all:
I have GALAXY installed in a UNIX server. BOWTIE works fine but TOPHAT and
CUFFDIFF crash upon starting.
In the case of TOPHAT, I noticed that GALAXY has a 1.5.0 version
integrated, while the TOPHAT website claims the latest version is 1.4.1.
My question is which are the best/appropiate
Nick,
I apologize if this is covered in documentation or help threads. searched
and it seemed it was not. I have several illumina rna-seq data sets that
should be directional. It seems the directionality is very good, based on
the visualization. First question is; in the visualization
Hi Stephen,
The options in the prior post are still current for the Galaxy main
server, however a direct method is something the team would like to
consider. I have opened a ticket a bitbucket to track progress:
I am using Galaxy main site to analyse MiSeq data of pooled samples.
Essentially the run produces 3 fastq files consisting of R1, R2 read files and
a separate index file. They are in the format below.
R1: @M00132:6:0-A0JG4:1:1:18014:1842 1:N:0:0
I used FASTQ groomer on a 29 Gb Illumina 1.5+ FASTQ file to go from
Illumina 1.3-1.7+ to Sanger and it is still processing after over 30
hrs. Is this a normal time frame for a FASTQ file this size ?
Matthew
The information in this e-mail is intended only for the person to whom it is
Phil,
we also have a MiSeq and currently experienced the same phenomenon how to
demultiplex.
We have our local galaxy instance and wrote some scripts to efficiently
demultiplex the sample. However, you FIRST need to convert on the MiSeq the
primary fastq into a (in their view) multiplex
Matthew,
yes we have seen such kind of long runs before (depending on server load).
Happy most of our reads are now in 1.8+ format.
You can parallelise the process by splitting the file in 4 or 6 and submit for
grooming and afterwards merge them again...
Alex
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