Re: [galaxy-user] tophat issues

[Jennifer Jackson]

Hello Miro,

It sounds like perhaps the datatype is not being assigned correctly, 
which may mean that they quality scores are not scaled properly. To 
double check both, see the instructions in our wiki here:

http://wiki.galaxyproject.org/Support#Dataset_special_cases

If you still need help after this, please write back to share a history,

Best,

Jen
Galaxy team

On 11/29/13 5:49 AM, miroslav.sotak wrote:

To whom it may concern

I do have a problem with tophat. I can easily put fastq data to 
history and according to RNA-seq Analysis Exercise provided by 
Jeremy. We checked the type of Ascii ofset for the quality estimation. 
I tried even quality data converter set to 33 (we do have data of 
this ASCII offset from 2 different sources) but tophat for Illumina 
simply can not read the data before and even after quality format 
converter. We do not have any idea what is going on. I am logged in 
Galaxy with current email, can you check my data and is there any 
converter for quality offset?


Sincerely
Miro Sotak
___
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/

To search Galaxy mailing lists use the unified search at:

 http://galaxyproject.org/search/mailinglists/


--
Jennifer Hillman-Jackson
http://galaxyproject.org

___
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/

To search Galaxy mailing lists use the unified search at:

 http://galaxyproject.org/search/mailinglists/

[galaxy-user] tophat issues

[miroslav.sotak]

To whom it may concern

I do have a problem with tophat. I can easily put fastq data to 
history and according to RNA-seq Analysis Exercise provided by Jeremy. 
We checked the type of Ascii ofset for the quality estimation. I tried 
even quality data converter set to 33 (we do have data of this ASCII 
offset from 2 different sources) but tophat for Illumina simply can 
not read the data before and even after quality format converter. We do 
not have any idea what is going on. I am logged in Galaxy with current 
email, can you check my data and is there any converter for quality 
offset?


Sincerely
Miro Sotak
___
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/

To search Galaxy mailing lists use the unified search at:

 http://galaxyproject.org/search/mailinglists/