This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Introns In Transcripts

Hello, I would like to know how I could find positions and lengths of introns in all transripts with exactly 4 introns. Could anybody help me? I want to use human newest assembly, but I'm not sure which group, track and table I should use for transcripts. And I can't find filter for 4 introns. Is something like that possible to find?

Thank you

ucsc
• 1,922 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by kadlik1989 • kadlik1989

1 answer

just select the transcripts having 5 exons:

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" | gunzip -c | awk '($8==5)'

see

How to download all the introns from UCSC

for more informations.

• 129 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this