Hello,

I recently ran featureCounts with fractional multimapping and found that one of the rows in the output table contains a blank Geneid. There are multiple chromosomes and start/stop coordinates assigned to this mystery feature, however, I'm having a hard time understanding why it is blank.

I generated a custom annotation using IsoQuant and long-read sequencing data. I did not find any missing gene names or placeholders within the custom annotation.

This is from a 2X2 RNA-sequencing experiment looking at gene expression in the deer mouse placenta.

featureCounts -O -M --fraction -p -F GTF -t transcript -T 24 -a OUT.extended_annotation.gtf \
-o ../FeatureCounts_Ext_MultimapFrac/EP_Pman_ExtMMFrac_readcounts.txt \
*.bam

Thank you!