Hi Jody,
I have a question regarding genes.bed.
I tried to reproduce the coordinates in genes.bed using the GFF provided in the TB-Profiler repository. The gene coordinates in this GFF are consistent with the coordinates I obtain from the NCBI GTF, but they differ from the coordinates in genes.bed.
In particular, the coordinates in genes.bed appear to extend upstream of the annotated gene boundaries. For genes on the + strand, the BED start coordinate extends upstream, while for genes on the − strand, the BED end coordinate extends upstream.
Could you clarify how the coordinates in genes.bed are defined? Does genes.bed intentionally include upstream/promoter regions, or is there another reason for the difference from the gene coordinates in the GFF?
Thanks!
Walter
Hi Jody,
I have a question regarding genes.bed.
I tried to reproduce the coordinates in genes.bed using the GFF provided in the TB-Profiler repository. The gene coordinates in this GFF are consistent with the coordinates I obtain from the NCBI GTF, but they differ from the coordinates in genes.bed.
In particular, the coordinates in genes.bed appear to extend upstream of the annotated gene boundaries. For genes on the + strand, the BED start coordinate extends upstream, while for genes on the − strand, the BED end coordinate extends upstream.
Could you clarify how the coordinates in genes.bed are defined? Does genes.bed intentionally include upstream/promoter regions, or is there another reason for the difference from the gene coordinates in the GFF?
Thanks!
Walter