This is a test version of Biostars. For the public version, visit https://www.biostars.org.
format the gtf file

Hi there, I have a gtf file. Could some one let me know how to move the third column with "transcript" to the first line of each gene block with the same gene id?

Thanks so much!

enter image description here

gtf
• 1,892 views • link
updated by Ram Ram • written by bright602 • bright602

1) do not use excel.

enter image description here

2) why would you want to do this ?

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Do not post the images of the data.

• 0 views • link
written by cpad0112 cpad0112

2 answers

Here several tools that can help you https://agat.readthedocs.io/en/latest/topological-sorting-of-gff-features.html

• 0 views • link
written by Juke34 Juke34

You want to do this in excel? Rename all transcript to AAA_transcript in col 3, sort by coordinate and then by feature type (col 3), rename back. You can implement something similar in Python, but I'm not sure it's worth the effort.

Also not sure why you want this but it's certainly not common practice, so there's unlikely a tool for this.

• 0 views • link
written by Carambakaracho Carambakaracho

Log in to answer this question.

More posts like this