Ns126:Calendar/NOTES/2015-10-16: Difference between revisions

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>Shicheng
(Created page with "==Missing value in MHL matrix== *1, in the line 169 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl in TSCC *the methylation haplotype were not output. therefore, eve...")
 
>Shicheng
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Line 8: Line 8:
  my @unmethylated_haps= ("T", "TT", "TTT", "TTTT", "TTTTT");
  my @unmethylated_haps= ("T", "TT", "TTT", "TTTT", "TTTTT");
  my @methylated_haps= ("C", "CC", "CCC", "CCCC", "CCCCC");
  my @methylated_haps= ("C", "CC", "CCC", "CCCC", "CCCCC");
my @unmethylated_haps= ("T", "TT", "TTT", "TTTT", "TTTTT","TTTTTT","TTTTTTT");
my @methylated_haps= ("C", "CC", "CCC", "CCCC", "CCCCC","CCCCCC","CCCCCCC");
it means the haplotype whose length is longer than 5 would be ignore.
* Therefore, actually, we only consider the haplotype whose length is 4 and 5.

Revision as of 18:06, 16 October 2015

Missing value in MHL matrix

  • 1, in the line 169 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl in TSCC
  • the methylation haplotype were not output. therefore, even we remove the mentioned constraint, the methylation haplotype would be longer than 3.
  • 2, In the line 26 and 27 of /home/k4zhang/bin/mergedBam2hapInfo_WGBS_25Jun15.pl
my @unmethylated_haps= ("T", "TT", "TTT", "TTTT", "TTTTT");
my @methylated_haps= ("C", "CC", "CCC", "CCCC", "CCCCC");
my @unmethylated_haps= ("T", "TT", "TTT", "TTTT", "TTTTT","TTTTTT","TTTTTTT");
my @methylated_haps= ("C", "CC", "CCC", "CCCC", "CCCCC","CCCCCC","CCCCCCC");


it means the haplotype whose length is longer than 5 would be ignore.

  • Therefore, actually, we only consider the haplotype whose length is 4 and 5.