Re: [galaxy-user] Problem Loading History Pane
Hello Lizex,
The utility tools from Tophat are not included with Galaxy, so that is
perhaps why you are having trouble creating junctions files, but I am
wondering if you need them at all.
You mention that you have different sequence types from different
samples. These represent different conditions? Or some do and others are
replicates or complete replacements for the originals (the re-sequenced
data)?
For data representing different samples/conditions, you would not want
to map the data together with Tophat or run it together in Cufflinks.
Even replicates are not mapped in the same Tophat job, although they are
included in the same Cufflinks job. The tool authors have an opinion
about the value of replicates - so be sure to read about that at the
Cufflinks web site.
http://cufflinks.cbcb.umd.edu/howitworks.html#reps
The first time different conditions would be in the same job would be at
the stage where Cuffmerge is run, to prepare for Cuffdiff - where the
differential expression analysis would take place. This is past the
stage where individual reads are involved.
Our RNA-seq tutorial is here:
https://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
And several donated by the Galaxy community are here:
http://wiki.galaxyproject.org/Learn#Other_Tutorials
But the best resource is the paper from the tool authors ("Protocol"):
http://tophat.cbcb.umd.edu/manual.html
http://cufflinks.cbcb.umd.edu/manual.html
In the end, you may decide that some of the complexity of your data can
be reduced by dropping some datasets, to simplify and achieve the same
overall results, or perhaps even improved results. In general, I think
it is probably safe to say that the less "done" to prep expression data,
and certainly the more homogeneous it is, the better the result. But
this is your decision.
Good luck with your project. Next time when asking a question, please
open a brand new email message and start a new thread, not reply to an
existing thread and just change the subject line. This helps us with
tracking and is appreciated.
Thanks!
Jen
Galaxy team
On 2/16/13 5:23 AM, Lizex Husselmann wrote:
Dear all
I have in my project single end reads (50 bp) for some samples and
paired end reads (100 bp frw and rev) for the other samples. I had to
re-sequence some of the samples of which I have paired-end reads.
However the re-sequence data I receives is single-end reads of 250 bp.
Tophat wont allow mapping single and paired-end reads together. It says
the result will look bad. They do mention that you can convert the
junctions.bed file (output of Tophat) with bed_to_juncs using the -j
option. I quote for TopHat manual "run TopHat on the 2nd set of reads
using the -j option to supply the junctions file produced by be_to_juncs
in the previous step". This is supposed to work but I didn't get it to
work. Any suggestion on how I should go about analyzing this data?
Kind regards
Lizex
>>> Nate Coraor 02/15/13 5:48 PM >>>
On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote:
> To whom it may concern:
>
> The History panel on the right side of the Galaxy page is taking a
very very long time to load. Also, when it does load, I have tired to
save my .bam files and the transmissions gets truncated to ~7000kb -
8000kb of data. All of my .bam files are several GB.
>
> Some times, when I retry tor download the data, it succeeds and other
times it is again truncated. The size of the truncation may be different
for the same file on the retry attempt.
>
> Is there a problem with Galaxy?
Hi Mike,
There are some performance problems with the Main site that we are
currently investigating Thanks for the information and we apologize for
the problems.
--nate
>
> Thanks,
> Mike
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Re: [galaxy-user] Problem Loading History Pane
Dear all I have in my project single end reads (50 bp) for some samples and paired end reads (100 bp frw and rev) for the other samples. I had to re-sequence some of the samples of which I have paired-end reads. However the re-sequence data I receives is single-end reads of 250 bp. Tophat wont allow mapping single and paired-end reads together. It says the result will look bad. They do mention that you can convert the junctions.bed file (output of Tophat) with bed_to_juncs using the -j option. I quote for TopHat manual "run TopHat on the 2nd set of reads using the -j option to supply the junctions file produced by be_to_juncs in the previous step". This is supposed to work but I didn't get it to work. Any suggestion on how I should go about analyzing this data? Kind regards Lizex >>> Nate Coraor 02/15/13 5:48 PM >>> On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote: > To whom it may concern: > > The History panel on the right side of the Galaxy page is taking a very very > long time to load. Also, when it does load, I have tired to save my bam files > and the transmissions gets truncated to ~7000kb - 8000kb of data. All of my > .bam files are several GB. > > Some times, when I retry tor download the data, it succeeds and other times > it is again truncated. The size of the truncation may be different for the > same file on the retry attempt. > > Is there a problem with Galaxy? Hi Mike, There are some performance problems with the Main site that we are currently investigating. Thanks for the information and we apologize for the problems. --nate > > Thanks, > Mike > ___ > 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: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:serviced...@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 000 604 Fax number : 0800 00 7788 Email address : a...@tip-offs.com Please Call me : 32840 Website: www.tip-offs.com For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za. ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] Problem Loading History Pane
On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote: > To whom it may concern: > > The History panel on the right side of the Galaxy page is taking a very very > long time to load. Also, when it does load, I have tired to save my .bam > files and the transmissions gets truncated to ~7000kb - 8000kb of data. All > of my .bam files are several GB. > > Some times, when I retry tor download the data, it succeeds and other times > it is again truncated. The size of the truncation may be different for the > same file on the retry attempt. > > Is there a problem with Galaxy? Hi Mike, There are some performance problems with the Main site that we are currently investigating. Thanks for the information and we apologize for the problems. --nate > > Thanks, > Mike > ___ > 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: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
