Extract 1KB upstream of specific gene in X chromosome

Question

[ahmedferoz20]

Hi,

first of all, i cant use any bedtools or samtools. I have to figure out the code.

My problem is i am given a gff file of chromosome X and also the fasta file for the chromosome. I have to extract a fasta file which have 1 kb upstream of each gene from chromosme X.

I will appreciate a lot if anyone can help me.

Regards-

Feroz

[finswimmer]

Hello ahmedferoz20 ,

I have to figure out the code.

so this is an assignment? What have you tried so far? What programming language do you like to use?

fin swimmer

[ahmedferoz20]

I can do the job with bedtools but i wanna learn and create an impression. I tried with linux but cant create e loop of 1kb upstream of each gene.

[Devon Ryan]

Then choose a programming language and write a custom program. You're not going to use standard Linux commands for this (well, you could but you'd be crazy to do so).

[ATpoint]

while [[ 1 > 0 ]]; do ./sarcasm.sh; done

[Kevin Blighe]

I think that it relates to this: Fasta file from a gff file