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 ---------- Forwarded message ---------- From: Moritz Juchler <juchler@stud.uni-heidelberg.de> 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-extrac... 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-mutati... and the matching *executed* history (with results) https://main.g2.bx.psu.edu/u/mj--/h/whole-exome-somatic-gene-mutation-extrac... 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 On 2 August 2013 18:50, Moritz Juchler <juchler@stud.uni-heidelberg.de>wrote:

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-mutati... and the matching *executed* history (with results)

https://main.g2.bx.psu.edu/u/mj--/h/clean-whole-exome-somatic-gene-mutation-...

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