only ~12% of assigned reads on featurecount
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.
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DGTool •
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diogo.moraes •
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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.