This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Bed file of union of all transcripts for a set of genes

Hi, I have a set of 100 genes and I want to obtain a bed file containing a union of all transcripts for each of those genes with hg19. IOW, for each gene, I want a bed file that contains the union of all reported transcripts for that gene. What is the fastest/best way to do so? Thanks!

transcripts gene exons
• 1,635 views • link
updated by michael.ante michael.ante • written by Floydian_slip Floydian_slip

Example input: a list of genes such as BRCA1 and ALDH1. Desired output: a bed file containing their transcripts. I understand there will be multiple lines for each for each of the transcript regions. Thanks!

• 0 views • link
written by Floydian_slip Floydian_slip

I was referring to pasting some real data examples, like a table that shows how things should look, not just words. You already explained with words in your question, but no coded solution yet because people do not know how exactly the data look like.

• 0 views • link
written by ATpoint ATpoint

1 answer

I'd grep a gtf with the gene list and use bedtools merge on the result.

• 0 views • link
written by michael.ante michael.ante

Log in to answer this question.

More posts like this