Daniel:Notebook/GenomeMiner/2013-8-28: Difference between revisions
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Script: [[File:Imp_count_mismatch.txt]] | Script: [[File:Imp_count_mismatch.txt]] | ||
'''Raw Error Counts''' | '''Raw Error Counts and Read Error Percentages''' | ||
Total read counts and numbers of reads with errors | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | |||
|- style="font-size:12pt" | |||
| align="center" width="65" height="30" valign="bottom" | | |||
|style="font-weight:bold" width="65" align="center" | Total reads | |||
|style="font-weight:bold" width="65" align="center" | Filtered reads | |||
|style="font-weight:bold" width="65" align="center" | Perfect match | |||
|style="font-weight:bold" width="65" align="center" | 1 ins/del | |||
|style="font-weight:bold" width="65" align="center" | 1 sub | |||
|style="font-weight:bold" width="65" align="center" | 2 ins/del | |||
|style="font-weight:bold" width="65" align="center" | 2 sub | |||
|style="font-weight:bold" width="65" align="center" | 1 ins/del & 1 sub | |||
|style="font-weight:bold" align="center" width="65" align="center" | 3+ | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" align="center" | Number | |||
| align="center" valign="bottom" | 20924455 | |||
| align="center" valign="bottom" | 15399065 | |||
| align="center" align="center" | 4801948 | |||
| align="center" align="center" | 3829283 | |||
| align="center" align="center" | 2242835 | |||
| align="center" align="center" | 1891019 | |||
| align="center" align="center" | 634644 | |||
| align="center" align="center" | 1506743 | |||
| align="center" align="center" | 492593 | |||
|- style="font-size:12pt" | |||
|style="font-weight:bold" height="15" align="center" | Percent | |||
| valign="bottom" | NA | |||
| align="center" valign="bottom" | 100 | |||
| align="center" valign="bottom" | 31.18 | |||
| align="center" valign="bottom" | 24.87 | |||
| align="center" valign="bottom" | 14.56 | |||
| align="center" valign="bottom" | 12.28 | |||
| align="center" valign="bottom" | 4.12 | |||
| align="center" valign="bottom" | 9.78 | |||
| align="center" valign="bottom" | 3.20 | |||
|} | |||
'''Error Percentages''' | '''Error Percentages''' | ||
Percent errors by base (ex 2% error means 1 in 50 bp will have an error) | |||
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | {| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext> | ||
|- style="font-size:12pt" | |- style="font-size:12pt" |
Revision as of 18:26, 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 | 2.03106318468037 |
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