• Intro

  • step_01
  • step_02
  • step_03
  • step_04
  • step_05
  • step_06
  • step_07
  • step_08
  • step_09
  • step_10
  • step_11
  • step_12
  • step_13
  • step_14
  • step_15
  • step_16
  • step_17
  • step_18
  • step_19
  • step_20
  • step_21
  • step_22
  • step_23
  • step_24

  • Credits

    UC Davis

    Step 15: SNPs/INDELs finding
    Saving results of previous run

    So far, we have detected SNP/INSEL candidates in our assembly comparing genotype "A" versus "B" and "C" (step 12). By similar way, using Python_CAP3_contig_poly_DIS_Feb_27_2004.py script we can compare two remaining combinations: genotype "B" versus "A" and "C"; and genotype "C" versus "A" and "B".

    Every time when we execute Python_CAP3_contig_poly_DIS_Feb_27_2004.py script, three new files with default names (deletions.good, insertions.good and substitutions.good) will be generated. If we want to save results of previous run we need to save them under different names. For example, save three files of previous run: deletions.good, insertions.good and substitutions.good as A_vs_BC_deletions.good, A_vs_BC_insertions.good and A_vs_BC_substitutions.good

    $ cp deletions.good A_vs_BC_deletions.good
    $ cp insertions.good A_vs_BC_insertions.good
    $ cp substitutions.good A_vs_BC_substitutions.good

    Then we are ready to run Python_CAP3_contig_poly_DIS_Feb_27_2004.py again.