This is a test version of Biostars. For the public version, visit https://www.biostars.org.
make IGV not to show chromosomes

I used genometools to sort a gff3 file, there are chromosomes coordinates in the sorted file. When I visualize this file in IGV, it shows the chromosome as a sequence as well. This makes it hard to distinguish between genes and other features. Is there a way to not show chromosomes in IGV? or the GFF file can be edited.

PS: I do not want to go and remove individual chromosome features from gff file.

I do not want to see the topmost blue line(chromosome) in the screenshot: enter image description here

igv genometools
• 1,735 views • link
written by Lalit • Lalit

Post a screenshot of what you are looking for (highlight parts you don't want to see).

• 0 views • link
written by GenoMax GenoMax

Added now. Thanks.

• 0 views • link
written by Lalit • Lalit

1 answer

If the chromosome is a feature in the GFF file, then it might be the easiest to remove them from the file?

Maybe something like grep -v "chromosome:" original.gff > modified.gff already does the job, but it may also be slightly more complicated depending on the naming scheme etc.

• 0 views • link
written by Matthias Zepper Matthias Zepper

Thanks removing chromosome from sorted gff file with the above command worked.

• 0 views • link
written by Lalit • Lalit

Then you can accept this answer (green check mark) to provide closure for this thread.

• 0 views • link
written by GenoMax GenoMax

Yeah done, didn't know this, thanks again!

• 0 views • link
written by Lalit • Lalit

Log in to answer this question.

More posts like this