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sum of each read assorted by length do not match with total reads number #67

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Seongmin-Jang-1165 opened this issue Oct 1, 2024 · 0 comments

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@Seongmin-Jang-1165
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Hello

i ran MinION_QC for analyze Direct RNA seq data. SQK-RNA004 kit is used and basecalled with DORADO. i added num_events_template column filled with zeroes according to issue #65

in summary.yaml, i found that the total read number is not equal to the sum of reads number assoretd by read length. do you have any idea about this problem..?

input file: summary_simplebasecall.txt
All reads:
total.gigabases: 0.2509179
total.reads: 195196
N50.length: 4130.0
mean.length: 1285.5
median.length: 447.0
max.length: 427305.0
mean.q: 6.2
median.q: 3.8
reads:
'>10kb': 2864
'>20kb': 1386
'>50kb': 499
'>100kb': 164
'>200kb': 38
'>500kb': 0
'>1m': 0
ultralong: 589.0
gigabases:
'>10kb': 0.0982018
'>20kb': 0.0776404
'>50kb': 0.0503026
'>100kb': 0.0272691
'>200kb': 0.0102906
'>500kb': 0.0
'>1m': 0.0
ultralong: 0.0545351
Q>=7:
total.gigabases: 0.0993263
total.reads: 44165
N50.length: 22152.0
mean.length: 2249.0
median.length: 461.0
max.length: 415309.0
mean.q: 14.8
median.q: 14.2
reads:
'>10kb': 1686
'>20kb': 876
'>50kb': 336
'>100kb': 118
'>200kb': 26
'>500kb': 0
'>1m': 0
ultralong: 442.0
gigabases:
'>10kb': 0.062837
'>20kb': 0.0514915
'>50kb': 0.0348353
'>100kb': 0.0197696
'>200kb': 0.0071883
'>500kb': 0.0
'>1m': 0.0
ultralong: 0.0395123
notes: ultralong reads refers to the largest set of reads with N50>100KB

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