Daniel:Notebook/GenomeMiner/2013-8-28: Difference between revisions

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'''Perl Script to Count Total Probe Number'''
'''Perl Script to Count Total Probe Number'''
perl script: [[File:Probecount.txt]]
  perl probecount.plx > probecount_idx10to13.txt
  perl probecount.plx > probecount_idx10to13.txt

Revision as of 22:34, 28 August 2013

HL155

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Slim Indexing Analysis

Counted Errors Using Modified Perl Script from Matt

Script: File:Imp count mismatch.txt

Raw Error Counts and Read Error Percentages

Total read counts and numbers of reads with errors

  Total reads Filtered reads Perfect match 1 ins/del 1 sub 2 ins/del 2 sub 1 ins/del & 1 sub 3+
Number 20924455 15399065 4801948 3829283 2242835 1891019 634644 1506743 492593
Percent NA 100 31.18 24.87 14.56 12.28 4.12 9.78 3.20

Error Percentages

Percent errors by base (ex 2% error means 1 in 50 bp will have an error)

  Mycroarray Slim Error %
Error Rate 2.03
Insertions 0.11
Deletions 1.18
Substitutions 0.75

Counting Results From Index 10-13

Print Only 3rd Column

awk '{print $3}' hrcp_sortfilt_slimindex_eq.sam > readlist.txt

Perl Script to Count Total Probe Number

perl script: File:Probecount.txt

perl probecount.plx > probecount_idx10to13.txt