Question: Fwd: Hcc Analysis Pipeline
0
Enis Afgan • 690 wrote:
Hi Moritz,
I'm forwarding your message to galaxy-user mailing list and Jennifer
from
Galaxy. Between the two, you should be able to get some help because
unfortunately this is not my area of expertise so I'm afraid I won't
be of
much help.
Good luck,
Enis
Date: Fri, Aug 2, 2013 at 6:52 PM
Subject: Re: HCC Analysis Pipeline
To: enis.afgan@irb.hr
Sorry Mr. Afgan, I messed up with the history. This is the current
one:
https://main.g2.bx.psu.edu/u/mj--/h/whole-exome-somatic-gene-mutation-
extraction-1
Or you just ignore the older message, I included the message above:
Dear Sir Afgan,
I am Moritz Juchler from University Heidelberg. I read through your
slides
for Bioblend and noticed that maybe you could help me with my problem.
For
my Bachelor thesis I have to setup GalaxyProject to find SNP's in
genomes
from hcc patients. I have a server on which I installed Galaxy
locally,
since we have a) very large files (>30GB per patient) and b) the data
is
protection sensitive.
My goal is to do the first 5 steps of this pipeline:
http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf (page
2)
from this paper:
http://www.nature.com/ng/journal/v44/n6/pdf/ng.2256.pdf
This is my current workflow:
https://main.g2.bx.psu.edu/u/mj--/w/workflow-whole-exome-somatic-gene-
mutation-extraction
and the matching *executed* history (with results)
https://main.g2.bx.psu.edu/u/mj--/h/whole-exome-somatic-gene-mutation-
extraction-1
My question is: Am I going in the right direction? I really dont know
if
I'm doing the correct steps :( Are there any links or papers that
explain
which specific tool I have to use for the first five steps?
Of course if you do not have the time to answer my question, please
refer
me to someone who can answer the question and maybe has the time for
it.
Best
Moritz