GeneFull Mapping Discrepancy

[mattg478]

Hello,

I had multimapping issues with my genome and my split-seq snRNA reads.
To limit this I have used a 'pseudo' transcriptome as my index.
I extracted the whole gene sequences and used these as the chromosomes.
I modified the corresponding GTF features so that the positions are relative to the gene start positions.

This dramatically improved my mapping, 73% of reads mapped uniquely.
However, I used --soloFeatures GeneFull and the summary.csv indicated that only 49% of reads mapped to GeneFull while 99% mapped to the Genome

As my reference was a transcriptome GeneFull = Genome and my GTF is specifically set up so that no base pairs are not included in a gene feature.

How then could I have this discrepancy that 50% of my reads mapped to somewhere in the genome that is not a gene, when the whole genome is genes...?

Any help is greatly appreciated
Thank you,
Matthew