GFF Parser to format gff file to contain chromosome,gene.starting-position and ending position

Question

[chevivien]

Hallo?Is their a tool to parse gff3 file ,such that the file will contain the following

Chromosome       gene          starting_position              ending _position

[Ashutosh Pandey]

A simple awk one liner may do what you want. Can you paste a few lines from your gff3 file or an you tell from where you downloaded your file. If your aim is to get the transcription start and end positions of transcripts then you can also try the following command on unix system.

mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e "select name,name2,chrom,strand,txStart,txEnd from refGene" > Refseq2Gene.txt

[ahmedferoz20]

I want to extract chromosome x from a gff3 file. How could i do this?

[ATpoint]

Please do not ask questions in other threads. As I said in your other thread, did you do any googling? Extract chr from gff would have this Biostars post as the top hit.