Question: How to get arabidopsis sequences from genome coordinates
0
gravatar for dorota.komar
2.3 years ago by
dorota.komar10
dorota.komar10 wrote:

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.

macs2 sequence • 857 views
ADD COMMENTlink written 2.3 years ago by dorota.komar10

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).

ADD REPLYlink written 2.3 years ago by Macspider2.9k
2
gravatar for PoGibas
2.3 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

I would use bedtools getfasta. You will need:

  • Arabidobsis genome (fasta format)
  • Regions of interest (bed format - you already have this)
ADD COMMENTlink written 2.3 years ago by PoGibas4.8k

Moved to an answer ;)

ADD REPLYlink written 2.3 years ago by WouterDeCoster40k

And now marked accepted.

ADD REPLYlink written 2.3 years ago by WouterDeCoster40k
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