Question: troubles with exon coordinate extraction from ucsc
0
gravatar for Eugene A
2.3 years ago by
Eugene A80
Eugene A80 wrote:

May be this is some misunderstanding from my side but I failed to figure it out so far.

I'm trying to extract exons coordinates for given set of genes (in bed format) from UCSC, which seems to be a straite forward task.

here the one line example from the bed file (the coordinates are in hg38):

1   156815640   156881850   NTRK1   ENSG00000198400

the problem is - that if I insert the given coordinates (chr1:156,815,640-156,881,850) in the "position" field here (https://genome.ucsc.edu/cgi-bin/hgTables) and then hit "get output" button with "exon + 0" options I'm getting following bed file back:

chr1    156806242   156806573   uc001fqe.3_exon_0_0_chr1_156806243_r    0   -
chr1    156807174   156807345   uc001fqe.3_exon_1_0_chr1_156807175_r    0   -
.
.
. 
chr1    156880448   156880539   uc057mdn.1_exon_1_0_chr1_156880449_f    0   +
chr1    156881456   156881850   uc057mdn.1_exon_2_0_chr1_156881457_f    0   +

As one can notice the first exon starts earlier (156806242) then my initial interval (156815640) so I'm getting several irrelevan exons. Maybe someone can explain me why does it happens and how I can evoid it?

Best, Eugene

ADD COMMENTlink modified 2.3 years ago by _r_am31k • written 2.3 years ago by Eugene A80
1

Maybe someone can explain me why does it happens

may be the ucsc uses the whole transcript as the initial location

and how I can evoid it?

bedtools intersect
ADD REPLYlink written 2.3 years ago by Pierre Lindenbaum131k

Thanks! Probably I indeed will work around it. I just naively thought that getting the exon coordinates for set of genes from the ucsc should be one step procedure.

ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by Eugene A80

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

ADD REPLYlink written 2.3 years ago by _r_am31k

Thanks! I'm new to biostar so I did not know about that option.

ADD REPLYlink written 2.3 years ago by Eugene A80
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