Daniel:Notebook/GenomeMiner/2013-8-28: Difference between revisions
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[[Daniel:Notebook/GenomeMiner|Back to Calendar]] | [[Daniel:Notebook/GenomeMiner|Back to Calendar]] | ||
==Slim Indexing Analysis== | ==Slim Indexing Analysis ([[Daniel:Notebook/GenomeMiner/2013-8-27|Started 8/27/2013]])== | ||
'''Counted Errors Using Modified Perl Script from Matt''' | '''Counted Errors Using Modified Perl Script from Matt''' |
Revision as of 23:23, 28 August 2013
HL155
Slim Indexing Analysis (Started 8/27/2013)
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.pngDiscussion
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.