Support #90
QC of aligned reads
Description
A QC report was generated by MultiQC. All samples need to be checked to make sure there were no problems and the data is of sufficient quality.
History
Updated by Jon Ambler almost 6 years ago
- Tracker changed from Bug to Support
- Subject changed from QC of aligner reads to QC of aligned reads
- Status changed from New to In Progress
- % Done changed from 0 to 30
The QC looks good, but there are a few samples with results that warrant further investigation. Some samples also had much greater sequencing depth.
Sample pe_sense pe_antisense failed
GSH-N-003-d14_CL100111633_L2_1 0.0011 0.0189 0.98
Reason: Almost all reads were undetermined in their strandedness
Also borderline:
GSH-KD-008-S1_CL100110984_L1_1 0.0068 0.5686 0.4245
GSH-NS-003-d14_CL100111635_L2_1 0.0253 0.4826 0.4922
A meeting was held with Relebohile to discuss the results.
Updated by Jon Ambler almost 6 years ago
When the differential expression analysis was run, the samples were clustering in two distinct groups.
Looking into the QC data again and seeing what was defining the clusters, it seems the problematic reads all have a higher "percentage assigned" value. They did not have more reads, but a higher proportion of the reads were aligning to features.
I am investigating this further, and will email the sequencing facility to see if they have an idea of what is causing this.
Updated by Jon Ambler over 5 years ago
- Status changed from In Progress to Resolved
- % Done changed from 30 to 100
The distinction appears to be as a result of tissue vs cell culture samples.