%week%12,%lecture%23% - pennsylvania state …ebola- snp-2014 km034562 03676 03680 03686 03687 03683...

2014  -­‐  BMMB  852D:  Applied  Bioinforma9cs  

   Week  12,  Lecture  23  

István  Albert    

Biochemistry  and  Molecular  Biology    and  Bioinforma9cs  Consul9ng  Center  

 Penn  State  

Redoing  the  SNP  calling  in  the  Ebola  paper  

•  Find  the  supplementary  material  

•  Download  the  SNP  calls  they  make  

Get  the  supplemental  informa9on  

Visualize  their  SNP  calls  

In  class  demonstra9on  

•  See  suppor9ng  class  website  for  code  

•  Formalize/understand  each  step  that  you  need  to  do  

•  Collect  the  requirements  and  enumerate  the  steps  

Tools  that  write  commands  

Some9mes  it  can  be  handy  to  write  a  tool  that  generates  a  series  of  commands.      

You  can  save  and  share  the  script  with  others  and  can  be  rerun  with  ease.  

Even  a  subset  of  the  data  may  capture  most  relevant  features  

Homework  23  

•  Call  snps  from  an  SRA  file  that  corresponds  to  one  sample  of  the  Ebola  genome.  

•  Compare  your  calls  with  those  generated  by  the  authors.  

•  Hint:  make  sure  to  use  the  same  reference  genome