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

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===Discussion===
At first I was a bit confused by these results, especially the pie charts.  There are now more zeros and over-amplifications present, although there are fewer reads used.  But I remembered I used the phred 64 flag, which is more stringent, so that probably threw out some data.

Revision as of 23:22, 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

Counts

Compare with full sequencing index

Histograms

Probe counts. Normalization for x axis is based on the expected number of reads, calculated by dividing the total number of reads for a given set by the total number of probes in that set. One indicates the probes were amplified more or less linearly, <1 means they were underamplified, and >1 means the probe was overamplifed. File:Probehist HL155 idx10to13.png

Pie Chart Statistics

Pie chart showing probe count statistics. Probe counts are divided into 3 classes: 0 reads, over-amplified (described as >5x the expected count), and normally amplified reads.

File:V6ProbeCounts Idx10to13.png|File:V4ProbeCounts Idx10to13.png

Discussion

At first I was a bit confused by these results, especially the pie charts. There are now more zeros and over-amplifications present, although there are fewer reads used. But I remembered I used the phred 64 flag, which is more stringent, so that probably threw out some data.