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" | &nbsp;
|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

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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 2.03106318468037
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