Daniel:Notebook/GenomeMiner/2013-8-28: Difference between revisions
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|- style="font-size:12pt" valign="bottom" | |- style="font-size:12pt" valign="bottom" | ||
|style="font-weight:bold" height="15" | Error Rate | |style="font-weight:bold" height="15" | Error Rate | ||
| align="center" | 2. | | align="center" | 2.03 | ||
|- style="font-size:12pt" valign="bottom" | |- style="font-size:12pt" valign="bottom" | ||
|style="font-weight:bold" height="15" | Insertions | |style="font-weight:bold" height="15" | Insertions | ||
| align="center" | 0. | | align="center" | 0.11 | ||
|- style="font-size:12pt" valign="bottom" | |- style="font-size:12pt" valign="bottom" | ||
|style="font-weight:bold" height="15" | Deletions | |style="font-weight:bold" height="15" | Deletions | ||
| align="center" | 1. | | align="center" | 1.18 | ||
|- style="font-size:12pt" valign="bottom" | |- style="font-size:12pt" valign="bottom" | ||
|style="font-weight:bold" height="15" | Substitutions | |style="font-weight:bold" height="15" | Substitutions | ||
| align="center" | 0. | | align="center" | 0.75 | ||
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Revision as of 18:27, 28 August 2013
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 | 2.03 |
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 probecount.plx > probecount_idx10to13.txt