I am a new user of Galaxy. I have received the data from an exome of 4 samples. I have two reads from each sample.
I have seen the Live Quickies, and I have a general idea that I want to do. I want to find every change in the exome of these samples. Then apply a filter to discard all the known SNPs. Finally I want to keep only the changes that are in common in the four samples and apply a scoring of possible pathogenic mutations (PhiloP, SIFT,…). Is it possible?
Anybody can help me by sending me a step by step protocol of how can I do this analysis?
And another question, could I do all these previous steps with each individual, independently, or should I do it with the four samples at the same time?
Thanks to all of you.
I look forward to hearing from you.
Eduardo Calpena Corpas, PhD Student
Instituto de Biomedicina de Valencia (IBV-CSIC)
C/Jaime Roig Nº 11
Valencia. E-46010 (SPAIN).
TEL: +34 96 339 1760. FAX:(+34) 96 369 0800