Hi
I want to obtain all the exons for mouse (mm10) with chromosome start_pos and end_pos followed by gene name. In UCSC table browser I have selected group: genes and gene prediction track; track: refseq genes; table refseq. In the output format tab i just selected custom track. I was getting the output as follows after i select the Exons plus and hit the get custom track in file button
chr1 134199221 134203590 NM_001039510_exon_0_0_chr1_134199222_r 0 -
chr1 134234014 134234412 NM_001039510_exon_1_0_chr1_134234015_r 0 -
chr1 134235227 134235431 NM_001039510_exon_2_0_chr1_134235228_r 0 -
However, i wanted it as
chr1 134199221 134203590 Adora1_exon_0_0_chr1_134199222_r 0 -
chr1 134234014 134234412 Adora1_exon_1_0_chr1_134234015_r 0 -
chr1 134235227 134235431 Adora1_exon_2_0_chr1_134235228_r 0 -
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written
by
ancient_learner
Can you please let us know from Where you got this dat ?
chr1 134199221 134203590 Adora1_exon_0_0_chr1_134199222_r 0 -
chr1 134234014 134234412 Adora1_exon_1_0_chr1_134234015_r 0 -
chr1 134235227 134235431 Adora1_exon_2_0_chr1_134235228_r 0 -
I understand this is different name of same gene !!
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written
by
always_learning
When I've wanted to substitute gene names for transcript IDs in a BED file, I used a dictionary I got from selecting "selected fields from primary and related tables" under output format in the table browser, then selecting only the "name" and "name2" fields on the page linked from there, which will provide a list of transcript IDs and their corresponding gene names. You may have to write a quick script to do the substitution in perl, R, etc.
Yeah i was doing the same thing but just wanted to know whether there is a method without code within the ucsc browser!
Not sure that there is one...that's two of us who'd like to know now!
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you need to select the
name2in the output (while selecting custom columns)!!Unless you know differently, I don't think it's possible to get exon coordinates in BED format with gene names instead of transcript IDs
I don't get custom column selection option here in this case