Map XLOCs in cufflinks assembly GTF to genes

Question

[oriolebaltimore]

Hi: I obtained merged.gtf file from cuffmerge. It has all XLOC. How can I map XLOC transcripts to genes from Ensembl Hg38.GTF.

I seemed to have done it before and now completely lost.

edit: Is this usage correct? bedtools intersect -a assembly.gtf -b Hg39.gtf -wa -wb > Merged_annotated.gtf

Thanks Adrian

[GenoMax]

Please include the command you used to run cuffmerge. Did you look at the -goption when you ran this.

-g/–ref-gtf

An optional “reference” annotation GTF. The input assemblies are merged together with the reference GTF and included in the final output.