Hi, I have the gtf file for mouse, and I wanted to create bed files for the 5' and 3' UTRs using this gtf file ( I know there is method using the UCSC Table website, but I want to generate using the GTF file itself).

As far as I know, information about the UTR regions is not explicitly stated in the gtf file. So, what would be a good strategy to extract these bed files from the gtf file?

Thanks!
Another [option][1].

    python extract_transcript_regions.py -i genes.gtf -o genes --gtf

now convert this blockbed (bed12) to bed6

    cat genes_3utr.bed | bed12ToBed6 -i stdin -n > genes_3utr_bed6.bed
    cat genes_5utr.bed | bed12ToBed6 -i stdin -n > genes_5utr_bed6.bed

  [1]: https://github.com/stephenfloor/extract-transcript-regions