Bedtools Flank Unexpected Behavior

Question

[gtasource]

Hi all,

I'm trying to use Bedtools Flank on a GTF file to extend all start coordinates 1000 upstream (with respect to the strand specificity) while keeping the end coordinate in tact. Here's the code:

bedtools flank -i gene_list.gtf -g sizes.genome -l 1000 -r 0 -s  > new_gtf.gtf

However, I've noticed that it's been changing both the start and end sequences in numerous cases. At first I thought that it was because some of the intervals extend the chromosome length, but I've seen it do this in situations where length is fine. Is my code correct? Any other software that can do this?

[Ram]

Not Doing What I Want

A more professional way to say that would be "unexpected behavior"

[gtasource]

Thank you. I went ahead and updated the title, and will keep this in mind for next time!

Answer 1

[ATpoint]

while keeping the end coordinate in tact

That is the problem. flank is the wrong subcommand, have a look at slop.

[gtasource]

Ah, stupid mistake! Thanks for pointing this out!