Ucsc Track Exonstarts/Exonends To Bed

Question

[PoGibas]

Example from UCSC track:

    bin    name    chrom    strand    txStart    txEnd    cdsStart    cdsEnd    exonCount    exonStarts    exonEnds
    73    TCONS_l2_00002368    chr1    -    89294    237877    237877    237877    2    89294,236614,    90404,237877,
    585    TCONS_l2_00002369    chr1    -    89550    91105    91105    91105    2    89550,90286,    90050,91105,

How to combine exonStarts with corresponding exonEnds to get only exon's bed file?

   chr1    89294    90404
   chr1    236614    237877
   chr1    89550    90050
   chr1    90286    91105

Answer 1

[Duarte Molha]

Install bedtools...

instead of trying to do that from the track, download the track as a bed12 file and use the command bed12ToBed6 to get all exon coordinates:

bed12ToBed6 -i UCSC_track.bed > UCSC_discrete_features.bed

or

bedtools bed12tobed6 [OPTIONS] -i UCSC_track.bed > UCSC_discrete_features.bed

If this is not possible a relatively simple awk script should do the trick:

awk 'BEGIN{OFS="\t"}{n_exons = split($10,e_starts,",");split($11,e_ends,",");for(i=1;i<n_exons;i++){print $3,e_starts[i],e_ends[i]}}' t.track > exons.bed

[PoGibas]

I was using bedtools for some time and didn't know it had such a cool feature.

[rmbannen]

I specifically created a biostars account so that I could upvote this reply. Thank you very much!

Answer 2

[AndreiR]

Hi, Think it may help you :
Exon coordinates of hg19 genome download