Hellp Tao,

When using a custom reference genome, the file must be in fasta format and the datatype must be set as fasta (use pencil icon to modify "Edit Attributes" as needed). Any fasta file is allowed, however those with simplified identifiers (no pipes "|", in particular) tend to have less problems with certain tools. If there are errors, the most likely cause is formatting.


If there are problems and you cannot resolve the format issue, please send a bug report associated with a failed mapping run using the custom reference genome. Use the green bug icon for the failed dataset when reporting the error (instead of screenshots).

I will watch for your bug report. If you use a different email than this one for your galaxy account, please note that in the bug report comments area so that I can link the two threads.

Thanks,

Jen
Galaxy team

On 8/15/11 10:38 AM, Peng, Tao wrote:
Hi Jen, I have RNA-seq data for 2 biologial samples loaded in to galaxy.
The samples are from human skin biopsies from genital herpes
reactivation. Using Tophat I will align the reads to human genome. But I
am NOT how to build genital herpes genome (HSV-2) and aligh reads to
HSV-2 genome? Any suggestion is greatly appreciated!

Thanks,


tao

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, August 12, 2011 11:54 AM
To: Peng, Tao; galaxy-b...@bx.psu.edu
Subject: Re: [galaxy-bugs] loading data

Hello,

Glad to hear that you were able to load your data.

When logged in, FTP loaded data will initially be in the FTP upload area

under the "Get Data ->  Upload" tool (in the center pane). From here,
load data into the history that you wish to work with. If you are not
sure where this is exactly, please note the graphics in the FTP wiki and

screencast.

As a reminder, please send all new and followup questions with a to or
cc to the mailing list, not to individual team members. This is
important for our team to be able to track and answer questions. We
would appreciate your helping out with this going forward.

Hopefully this helps.

Jen
Galaxy team

On 8/12/11 11:39 AM, Peng, Tao wrote:
Hi jen, I just finished FTP of R4 data set with 8.4 GB. Why can't I
see
the data on the right panel of galaxy after loggin in?

Tao

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Tuesday, August 09, 2011 3:26 PM
To: Peng, Tao
Cc: galaxy-b...@bx.psu.edu
Subject: Re: [galaxy-bugs] loading data

Hello Tao,

It sounds like the load works with an uncompressed file but is failing
when compressed? Perhaps there is a problem with the compression
itself.

We can't really help with this part of the process except to note
which
compression types we accept. The help wiki link again is:
http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

The final goal would be to have all of the data compressed and then
load

using FTP in a batch. If this takes too long to run, then the next
option is to run either a local or cloud install. Help can be found
at:
http://getgalaxy.org
http://galaxyproject.org/Admin/Cloud

Please send all questions related to local or cloud installations to
the

galaxy-...@bx.psu.edu mailing list and not to individual team members
or

to the galaxy-b...@bs.psu.edu mailing list.

Best wishes for your project,

Jen
Galaxy team

On 8/9/11 2:25 PM, Peng, Tao wrote:
If I up-load one file (uncompressed) at one time, I will have 4x8=32
files to up-load. Each file takes about 1 hour to load. This is
untenable. Any suggestion?

Thanks,


tao

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Tuesday, August 09, 2011 2:04 PM
To: Peng, Tao; galaxy-b...@bx.psu.edu
Subject: Re: [galaxy-bugs] loading data



On 8/9/11 1:55 PM, Peng, Tao wrote:
Hi Jen, if I have 8 fastq.gz files for each of my 4 samples, how
should
I load the data for analysis in galaxy?

Thanks,

tao

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Tuesday, August 09, 2011 1:31 PM
To: Peng, Tao
Cc: galaxy-b...@bx.psu.edu
Subject: Re: [galaxy-bugs] loading data

Hello Tao,

For your other question sent to me directly, Galaxy will accept only
one

file per archive, so sending a multi-file .gz will result in only
the
first file in the archive loaded into the "Get Data ->     Upload"
FTP
area.

Given the current issues, please try a restart. Log out of Galaxy
and
FileZilla (and restart your computer if possible). Then begin again,
testing with a single, uncompressed file. You do not have to be
logged
into your Galaxy account to load with FileZilla, but you will need
to
be

logged in to access the files on the "Get Data ->     Upload" form
after
upload is complete.

If this fails, perhaps try reinstalling FileZilla or even a
different
FTP client. This tutorial covers an alternative that can also be
used
from the desktop:
http://galaxyproject.org/Learn/Upload via FTP

If you do have more questions, please leave galaxy-b...@bx.psu.edu
on
the cc list so that our entire team can help contribute to replies.
This

may also be a question that you want to ask the larger user
community
at

galaxy-u...@bx.psu.edu, as this sounds like an external issue.
Another
user may have encountered this problem using a PC and have
suggestions.

Thanks!

Jen
Galaxy team

On 8/9/11 1:16 PM, Peng, Tao wrote:
Hi jen, I attached a screen shot of FileZilla. Do you know why the
top
panel says "disconnected from server" while the bottom panel
indicates
it is transferring the data?

Thanks,


tao

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Monday, August 08, 2011 4:55 PM
To: Peng, Tao
Cc: galaxy-b...@bx.psu.edu
Subject: Re: [galaxy-bugs] loading data

Hello Tao,

The loading times do seem to be long for the size of the files,
perhaps
the internet connection is the problem. That said, FileZilla can
restart

an FTP if it is interrupted and a message would be reported. I
didn't
see any restarts reported in the log in the screenshot you sent.

The compression is another place to look for a problem. You might
try
to

use an alternate compression or no compression and load that way.
Try
one file, through FileZilla, as a test to see if that performs
better.
Winzip can compress in a few different formats, .bz2 is also
accepted
by

Galaxy.

Hopefully one of these will work. Please keep galaxy-bugs in the cc
for
any follow-up so that our team can help contribute to replies,

Thanks,

Jen

On 8/8/11 4:04 PM, Peng, Tao wrote:
Hi jen, when I FTP 9 of the fasq.gz files (each about 350 MB) for
sample, the FTP program (FileZilla) keep coping the files again
and
again, this is strange to me. Do you know what went wrong here.

I attached a powerpoint slide that is the screen shot of FileZila
(R1_002.fasq.gz has been copied 3x so far??)

Thanks,


tao

-----Original Message-----
From: Jennifer Jackson [mailto:j...@bx.psu.edu]
Sent: Friday, July 29, 2011 1:20 PM
To: Peng, Tao
Cc: galaxy-b...@bx.psu.edu
Subject: Re: [galaxy-bugs] loading data

Hello Tao,

Our apologies, the public Galaxy instance at http://usegalaxy.org
has
been experiencing higher than usual usage the last few days. This
should

now be improved. Please try your FTP load again - it is the best
way
to
load files and the sizes you mention are well within the accepted
limits.

Thank you for your patience,

Best,

Jen
Galaxy team


On 7/29/11 9:47 AM, Peng, Tao wrote:
Hi I work at FHCRC in Seattle. I am trying to load the FASQ data
from
Illumina HySeq. I have 4 samples with 2.4 GB of seq data per
sample.
For
the overnight FTP, I can't even finish loading half of one
sample.
Is
there any faster way to load the data? Can GALAXY do the analysis
for
this type of large data?

Thanks,

tao











--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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