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Old 11-06-2018, 12:27 PM   #1
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Location: Germany

Join Date: May 2018
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Default mouse tumor whole Exome sequencing Analysis

Hi everyone,

i am a little bit new to tumor whole exome seq analysis and did it only once before for normal human samples using bwa and Gatk pipeline and now I want to do whole exome sequencing of "tumor biopsies" from 6 mice (3 Ko and 3 ctrl) and have a normal tissue sequence for one of the mice for each genotype. The main goal is to find difference in number and nature/patterns of mutations between the tumor samples from the ctl vs ko mice ( as non synonymous, synonymous, non coding, frequency of transitions, etc..)
as we believe the ko to be more protected (therefore should accumulate less number of mutation).
the sequence will be done on illumina Novaseq with 150 Pb.
I would like to know your suggested analysis workflow, especially that can be optimized to work on a rather small workstation (with 16 cores, 64 GB ram).

Thanks in advance.
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