Extract gff of a particular chromosome
I have a gff file that contains all the information from Chromosome 1 - Chromosome 14. But I need gff information on individual chromosome basis. For example, I am performing some experiment on Chromosome 11 and trying to visualize my result on IGV. When I load the gff file in IGV it is showing gene information of all the chromosome. How can I get the gff of only Chromosome 11?
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ahmedferoz20 •
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mhasa006
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mhasa006
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Why are you bothered by IGV showing you all chromosomes? You just need to double-click on the chromosome you are interested in to select and zoom to just that chromosome (or use the drop-down menu).
Hello, I was trying to grep chromosome X from a gff file. I have an output but it is empty. I am a beginner in this. Please help me.
Ok, you are not supposed to ask questions in other threads but before you refresh even more old ones, please show the output of
cut -f1 your.gff | sort -k1,1 | grep -v '^#' | uniq -cand post the command you used.hanks a lot. Sorry, I am not aware of it. I am still not getting a file with chromosome 'x' only. I have used grep chrX myfile.gff>chrx.gff
@ahmedferoz20 I deleted your comment because you added it as an answer instead of using
Add Reply.What is the output of
cut -f1 your.gff | sort -k1,1 | grep -v '^#' | uniq -cYep ok i ad doing it now.
grep chrX myfile.gff>chrx.gffto extract output of chrX.2 The output of the script you gave me is
I hope i followed your suggestion to get help.
What? A link to ncbi is for sure not the output.
head -n 20 your.gffwill also do.@ATpoint, I admire your patience.
We all were unexperienced at some point. I assume that the problem is that the chromosomes are labelled as 1,2,3...X rather than chr1,chr2,chr3...chrX, that is why I asked for the
cut -f1 your.gff | sort -k1,1 | grep -v '^#' | uniq -cbecause that will list the unique chromosome names.Thanks a lot. I got it. However, my next challenge is to create a fasta file from that chromosome x file. I have to create a fasta file which contain 1000bp upstream of each gene.
Thanks a lot. Sorry, I am not aware of it. I am still not getting a file with chromosome 'x' only.