How to get arabidopsis sequences from genome coordinates

Question

[dorota.komar]

Hi Guys, I want to play a little bit with my ChIP-seq results. I would like to see if there is any motif in the sequences where my TF is binding. I have MACS2 results with chromosome name, start and end position - do you know how to get the sequences for Arabidopsis from that? I have seen many answers about human genome, but I kind of cannot find a way to do that for Arabidopsis.

Thanks a lot for your help, Dot.

[Matteo Schiavinato]

If you're using a Linux terminal and you want just a couple of sequences, you can use cut -c (read man cut for details).

Answer 1

[PoGibas]

I would use bedtools getfasta. You will need:

• Arabidobsis genome (fasta format)
• Regions of interest (bed format - you already have this)

[WouterDeCoster]

Moved to an answer ;)

[WouterDeCoster]

And now marked accepted.