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markziemann / dee2

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
http://dee2.io
GNU General Public License v3.0
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Some of the QC metrics don't make sense #4

Closed markziemann closed 7 years ago

markziemann commented 7 years ago

Here are the metrics for ERR1521856 - mapping rates are >100%

QualityEncoding: Read1MinimumLength:101 Read1MedianLength:101 Read1MaxLength:101 Read2MinimumLength:NULL Read2MedianLength:NULL Read2MaxLength:NULL NumReadsTotal:48413790 NumReadsQcPass:15599846 QcPassRate:32.2219% PE_Read1_StarMapRateTest:36 PE_Read2_StarMapRateTest:NA PE_Read1_Excluded:FALSE PE_Read2_Excluded:FALSE MappingFormat:SE STAR_UniqMappedReads:17070762 STAR_Strandedness:Unstranded STAR_UnmappedReads:1265655 STAR_MultiMappedReads:28469676 STAR_NoFeatureReads:175369 STAR_AmbiguousReads:360374 STAR_AssignedReads:16535019 STAR_UniqMapRate:109.429% STAR_AssignRate:105.995% Kallisto_MappedReads:18057444 Kallisto_MapRate:115.754% QC_SUMMARY:'

markziemann commented 7 years ago

Looks like this has been fixed in the latest commit by fixing a bug in the way the available reads are counted.

QualityEncoding:
Read1MinimumLength:101
Read1MedianLength:101
Read1MaxLength:101
Read2MinimumLength:NULL
Read2MedianLength:NULL
Read2MaxLength:NULL
NumReadsTotal:48413790
NumReadsQcPass:46806093
QcPassRate:96.6793%
PE_Read1_StarMapRateTest:36
PE_Read2_StarMapRateTest:NA
PE_Read1_Excluded:FALSE
PE_Read2_Excluded:FALSE
MappingFormat:SE
STAR_UniqMappedReads:17070762
STAR_Strandedness:Unstranded
STAR_UnmappedReads:1265655
STAR_MultiMappedReads:28469676
STAR_NoFeatureReads:175369
STAR_AmbiguousReads:360374
STAR_AssignedReads:16535019
STAR_UniqMapRate:36.4712%
STAR_AssignRate:35.3266%
Kallisto_MappedReads:18057444
Kallisto_MapRate:38.5793%