This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How to get only the first introns in bed file format from UCSC Gene data?

Hi,

I am interested in learning more about the first introns of UCSC gene or RefSeq gene in the UCSC genome browser. However, there doesn't seem to be a way to extract only the first intron data in bed file format. I understand that I can get exons or introns using table browser but it does not seem to have an option to only look at all the first introns of the genes. Has anyone figured out a way to approach it? Thanks a lot.

Best,

genome
• 1,861 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by beichenw909 • beichenw909

1 answer

if I'm not wrong, this should do the job:

wget -O - -q "http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/refGene.txt.gz" | \
gunzip -c |\
awk -F '\t' '{nEx=int($9);if(nEx==1)next;split($10,S,/,/);split($11,E,/,/);printf("%s\t%d\t%d\t%s\n",$2,($4=="-"?E[nEx-1]:E[1]),($4=="-"?S[nEx]-1:S[2]),$2);}'
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pirerre,

That totally makes sense. Thank you so much.

Best

• 0 views • link
written by beichenw909 • beichenw909

if it works for you, close+validate this post by clicking the green mark on the left.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this