only ~12% of assigned reads on featurecount

Question

[diogo.moraes]

Hello

I am getting an unusual amount of unassigned reads on this data I am processing. One of the samples looks like this, which is not much different from the others

Status  T1.fq.gz
Status  T1.fq.gz
Assigned    8151393
Unassigned_Unmapped 8199336
Unassigned_Read_Type    0
Unassigned_Singleton    0
Unassigned_MappingQuality   0
Unassigned_Chimera  0
Unassigned_FragmentLength   0
Unassigned_Duplicate    0
Unassigned_MultiMapping 11888056
Unassigned_Secondary    0
Unassigned_NonSplit 0
Unassigned_NoFeatures   1639157
Unassigned_Overlapping_Length   0
Unassigned_Ambiguity    36784230

This is the first time I see this happening. Every other QC parameter seemed normal. I used the GRCh38 DNA assembly and GRCh38 gff3 from ENSEMBL.

This data comes from tumor samples and this is my first time analysing one, so I am not sure if it has something to do with it such a high number of mutations or chromosomal abnormalities.

[DGTool]

Would it be possible to post the tools and the commands you used for i.e. preprocessing, mapping and for featureCounts? It might help understand what the issue could be.