Question: How to get H3K4me1 FASTA file using UCSC genome browser?
gravatar for allyson1115ar
4.0 years ago by
allyson1115ar20 wrote:

I have H3K4me1 bed file that I would like to obtain its sequence using UCSC genome browser. There are many options provided. I'm using the following options: clade: mammal, genome: human, assembly: hg18, group: ?, track: ?

May I know what should I select for the group and track options? thanks.

histone chip-seq sequence ucsc • 965 views
ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by allyson1115ar20

It's probably easier to:

  1. Download the hg18 fasta file
  2. Install bedtools
  3. Use getfasta from bedtools with 1. and your BED file.

There are then no options to worry about clicking or limitations on the number of regions.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Devon Ryan95k
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