Make 1000bp windows upstream and downstream across TSS

[Tania Ghosh]

Hi,
I need to make windows of 1000bp upstream and downstream for each TSS for hg19. Is it possible by using bedtools?

Thanks

Tania

[m4merg]

If I got your task correctly, then you dont need bedtools for this. You only need to get all TSS positions for all genes (transcripts) using for example UCSC table browser and than just make bed from this using for example awk.

[Tania Ghosh]

Thanks for your suggestions!