A message sent earlier this week by me indicated that I could not connect
to Galaxy via Fetch to download data.
A reply indicated a glitch was fixed.
I then could connect with Fetch and I tried to transfer 4 x 16gb files and
the connection disconnected about 4 times.
Now, once again, I cannot connect with Galaxy online to transfer data.
Is this a problem that can be solved-either at my end or at Galaxy?
I want to calculate GC content of transcripts in the gtf file like this:
chr1 Cufflinks transcript 3 22 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1";
chr1 Cufflinks exon 3 10 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; exon_number "1";
chr1 Cufflinks exon 13 18 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; exon_number "2";
chr1 Cufflinks exon 20 22 1000 + . gene_id "CUFF.23955"; transcript_id "CUFF.23955.1"; exon_number "3";
and the genome sequence that transcript comes from is:
I have to calculate GC content of the transcript after getting the sequence of the transcript.
So how can I get the sequence of the transcript. In this case, it would be AGCGTCTC + ACGCGG + TAT, meaning
the transcript sequence would be AGCGTCTCACGCGGTAT.
Is it possible in the Galaxy?
Hi Jen and other galaxy-users,
I was using "Slice BAM" tool on Galaxy to get the alignment overlap with the
targeted intervals. After I got the output BAM file, I used "flagstat" to
get the detailed information of the output BAM file. What I got from
"flagstat" is as following.
"13704486 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
2989995 + 0 mapped (21.82%:-nan%)
13704486 + 0 paired in sequencing"
What's the QC-passed reads? What's the mapped reads? Should I only get the
mapped reads to the targeted intervals? I am very confused. Any help is
highly appreciated! Thanks a lot!
Yes, MEME is not on the Main server, but can be used in local, cloud, or
slipstream Galaxy installs. For throughput - there are a few
MEME-related repositories in the Tool Shed to choose from. How many
sequences each can process will likely vary and are related to the
hardware the Galaxy instance is run on. Contacting the tool authors is
one path or you can try testing using your actual data. Data composition
could be an important factor (not just the number of sequences).
For the Sequence Logo Generator, I do not know of a hard limit by the
tool itself, but as the recommended/supported input is ClustalW output,
that tool will most likely be setting the potential upper limit when
using the public Main Galaxy instance. Testing will be the best way to
learn the limits for your particular data (whether nucleotide or
protein), but the success range will be capped in the thousands, not
millions (and possibly lower, as length increases). If there is a memory
problem or the run time exceeds the limits on the public server, the job
will end with an error. Moving to a scaled up server, such as a cloud
Galaxy, will give you more control over these types of variables.
Some benchmarks are in the Clustal W publication:
If others would like to post benchmarks from their own experience, that
would be welcome!
On 9/11/13 2:51 PM, Boaz Shaanan wrote:
> Has the MEME module been taken out of the main galaxy server? Assuming
> it'll be back, what's roughly a recommended number of sequences to
> feed into MEME? It has a limit on the sequences that it can digest but
> I don't know what it is. Likewise, what's this limit for the Sequence
> Logo Generator?
> /Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben-Gurion University of the Negev
> Beer-Sheva 84105
> E-mail: bshaanan(a)bgu.ac.il
> Phone: 972-8-647-2220 Skype: boaz.shaanan
> Fax: 972-8-647-2992 or 972-8-646-1710 /
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org. Please keep all replies on the list by
> using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
> To manage your subscriptions to this and other Galaxy lists,
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I am interested the Galaxy and want to set up a local galaxy. Could you address me the PV of galaxy one day?
Email: liubiao(a)genomics.cn | M. +86 186 7677 1486
China National GeneBank http://nationalgenebank.org/en/index.html
Building No.11 | Beishan Industrial Zone | Yantian | Shenzhen China
I too have been repeatedly receving the FTP error as reads in the subject line of the email when trying to connect. I've done everything possible to end all connections, and still get this error.
Could you advise if there is any other step that I can take to reset connections? I had a file upload going, but it ended about half-way through and notified me to re-try login. I did try the log on again, and ended up receiving the FTP error message and have been unable to connect since (3 days ago).
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I am performing some RNA sequencing. I am using a gtf file as a reference annotation for the cufflink - cuffmerge steps. Then when I do the cuffdiff I find something strange. Where there is the gene name, the corresponding values (all of them!) are 0, where there is no gene name there are values of expression, fold change etc.
Does anyone have an idea of what is going on? I haven't find any similar question in the Galaxy archive.
Also, I tried to visualize my outputs (TopHat Cufflink Cuffmerge) using Trackster but it gives me an error. Is anyone experiencing the same problem?
My name is Pinkuan, and I have been analyzing some RNA-seq data these days,
but I confronted a problem when I did the visualization of the Tophat
recepted hits with the Trackster tool. When I add the data of Tophat
recepted hits to the visualization tool, there turns out to be an error
that I can not visualize the data. So, do you have any idea about how to
solve this problem?