How To Download All The Introns From Ucsc

Question

[Anima Mundi]

Hello,

I would to know how to download the FASTAs of all the introns from a given UCSC genomic assembly.

Answer 1

[Pierre Lindenbaum]

The following command line prints all the introns of the ucsc/knownGene table.

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz" |\
gunzip -c  |\
awk -F '   ' '{ exonCount=int($8);split($9,exonStarts,"[,]"); split($10,exonEnds,"[,]"); for(i=1;i<exonCount;i++) {printf("%s\t%s\t%s\t%s\t%s\tIntron_%d\n",$1,$2,$3,exonEnds[i],exonStarts[i+1],($3=="+"?i:exonCount-i));}}'

uc001aaa.3    chr1    +    12227    12612    Intron_1
uc001aaa.3    chr1    +    12721    13220    Intron_2
uc010nxq.1    chr1    +    12227    12594    Intron_1
uc010nxq.1    chr1    +    12721    13402    Intron_2
uc010nxr.1    chr1    +    12227    12645    Intron_1
uc010nxr.1    chr1    +    12697    13220    Intron_2
uc009vis.2    chr1    -    14829    14969    Intron_3
uc009vis.2    chr1    -    15038    15795    Intron_2
uc009vis.2    chr1    -    15942    16606    Intron_1
uc009vit.2    chr1    -    14829    14969    Intron_8
(...)

[Anima Mundi]

Very useful answer, thanks. I accepted Wen's solution because it is "ready to go".

Answer 2

[Wen.Huang]

UCSC table browser, select the appropriate track (e.g. some gene annotation), select output format "sequence", click "get output", select "genomic", there will be options to download "introns".

[Anima Mundi]

Thanks. Download started ;).