Hello,
I am new in using Galaxy and I am working on .bam files
generated by our sequencing platform, using the LifeScope
software associated to ABI 5500 sequencer. I uploaded my files
on a galaxy browser (
http://galaxy.raetschlab.org) and I
tried to run cufflink assemble and quantify reads expression
levels for each file. However, when I run cufflinks (using
default parameters) the output is an empty file.
What is going wrong? Should I use special parameters? Are
the .bam files generated by LifeScope suitable for cufflink
analysis or should I transform the xsq ABI output in a fastq
and then apply TopHat?
I thank you very much for your help
Davide
---
Davide Degli Esposti, PhD
Epigenetic (EGE) Group
International
Agency for Research on Cancer
Tel. +33 4
72738036
Fax. +33 4
72738322
150, cours Albert Thomas
69372 Lyon Cedex 08
France
------------------------------------------------------------------------------------------------
This message and its attachments are strictly confidential.
If you are
not
the intended recipient of this message, please immediately
notify the
sender
and delete it. Since its integrity cannot be guaranteed, its
content
cannot
involve the sender's responsibility. Any misuse, any
disclosure or
publication
of its content, either whole or partial, is prohibited,
exception made
of
formally approved use.
------------------------------------------------------------------------------------------------
___________________________________________________________
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/