Question

Stop Codons Human Genome

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8.8 years ago

c1toscano • 0

Hi, I wonder how to download the coordinates of all the stop codons on human genome. Thanks!

gene sequence • 1.6k views

ADD COMMENT • link updated 16 months ago by Ram 43k • written 8.8 years ago by c1toscano • 0

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Surprisingly, this isn't available via biomart. You can, however, just grep "stop_codon" from the GTF file if you download that from Ensembl or Gencode.

BTW, I'm posting this as a comment to not dissuade someone from posting the mysql/UCSC one liner.

ADD REPLY • link updated 16 months ago by Ram 43k • written 8.8 years ago by Devon Ryan 104k

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We all know who the "someone" is :-)

ADD REPLY • link updated 16 months ago by Ram 43k • written 8.8 years ago by Ashutosh Pandey 12k

Ram · Answer 1 · 2015-06-16

As a BED file, using UCSC known genes:

 curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz"  | gunzip -c | awk -F '\t' '{if(int($6)<int($7)) printf("%s\t%d\t%d\n",$2,($3 == "+"?int($7)-3:int($6)+0),($3=="+"?int($7):int($6)+2));}' | sort | uniq
chr10    100003912    100003915
chr10    100008677    100008679
chr10    100143554    100143556
chr10    100154948    100154950
chr10    100177320    100177322
chr10    100183361    100183363
chr10    100186935    100186937
chr10    100189291    100189293
chr10    100219330    100219332
chr10    100221542    100221544