Hello Dr. Linney,
This genome (multiple releases, including danRer7) is scheduled for the
next batch of genome processing. You will see the last two batches
published to the public Main instance first - sometime next week - and
this next batch update published around the start of April. (There
Can you add danrer7 as a reference genome for tophat2 for online Galaxy?
Its there for tophat for Illumina.
Elwood Linney
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
a
Hi Scott,
I am sorry that you have been having problems - and hope that I can
help.
I just tested FTP right now - and it is working for me. My guess is
that the server name being entered is incorrect. You want this to be
"usegalaxy.org" (not "usergalaxy.org"
Hi Sathya,
The SnpEff tool is set up at this time for annotation with the /C.
elegans/ WS220 genome only. Including human in the future on the public
Main server at http://usegalaxy.org is under current evaluation.
For now, use the tool in a local or cloud Galaxy instance, with the tool
inst
Hi Meike,
Our apologies for the server issues, these were transitory for a short
window but should be fine now.
The issue with history pane updates are unrelated to the
deletion/purging of data. The expectation is that the database can take
up to a few hours to update quota usage after perma
Hi Scott,
Is the 'Get Data -> Upload File' tool no longer functioning for you? Can
I help with using Main or is this on a local/cloud instance that needs
to be set up?
https://wiki.galaxyproject.org/Support#Loading_data
It is correct that the addition upload methods via the "Load Data"
proce
For all users:
The tutorial on uploading data is incorrect. I do not think they have
updated "how to upload data" yet.
Scott
Scott Tighe
Senior Core Laboratory Research Staff
Advanced Genome Technologies Core
NextGen Sequencing/Flow Cytometry
University of Vermont and Vermont Cancer Center
14
Hello,
I deleted some files, because I reached 100% of the data volume I could use; my
actual volume is 76 GB. I'm waiting now for an update from the server, that I
reduced the data volume and can continue with my analysis. But I got a red note
on the history for several times, that the update
I am quite new to RNA-seq analysis, but what I have learned so far is that
replicates are important. If you have this result with no replicates then
P-values are more or less meaningless. You can also gauge what is happening by
looking at the modelled read count output. If the counts are both
Hi Uma,
If you look under 'NGS Mapping' there is 'Map with Bowtie for SOLiD' and 'Map
with BWA for SOLiD'
They take fastq, but you can use 'NGS: QC and manipulation' > 'Convert' to
generate a fastq file from fastqc and qual files. Or at least you could for
SOLiD4 files.
Ian
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