Question: How to search for specific data in gff file
gravatar for Affan
6.0 years ago by
Affan290 wrote:

I am currently reading a paper which deals with the transcription factor Sp1 binding sites on Chr 1. In the methods section, they say that the genome wide positions of Sp1 binding sites were obtained from FANTOM 4.

I downloaded this file and added it as a custom track to the UCSC genome browser. It shows me (I think) all the transcription factors and their binding sites. But there are a lot, and I can't seem to find Sp1. They are named as example: "TF_binding_site_cage_181208AR-110574".

My question is, what kind of software would I need to use to obtain Sp1 data only? I'd like to extract Sp1 data only and then put it up as a custom track on the genome browser.

sequencing genome • 1.6k views
ADD COMMENTlink modified 6.0 years ago by Jeff Stafford50 • written 6.0 years ago by Affan290
gravatar for Jeff Stafford
6.0 years ago by
Jeff Stafford50 wrote:

Try this command in terminal (should extract all lines with "Sp1" to a new gff file):

grep -i 'sp1' your_GFF_file > sp1.gff

If that doesn't work try grepping for other names for your transcription factor.

ADD COMMENTlink written 6.0 years ago by Jeff Stafford50
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