Daniel:Notebook/GenomeMiner/2013-8-28
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HL155
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 | 2.03106318468037 |
Insertions | 0.10772186493141 |
Deletions | 1.17707730956392 |
Substitutions | 0.746264010185034 |
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 probecount.plx > probecount_idx10to13.txt