Generate .bed file with exon and intron indices
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3.8 years ago

Hi everyone, I'm wondering how I might generate the following file format.

chr1 24683494 24685032 ENST00000003583 utr3 0 r STPG1 ENSG00000001460
chr1 24685032 24685109 ENST00000003583 cds 0 r STPG1 ENSG00000001460
chr1 24685109 24687340 ENST00000003583 intron 0 r STPG1 ENSG00000001460
chr1 24687340 24687531 ENST00000003583 cds 1 r STPG1 ENSG00000001460
chr1 24687531 24696163 ENST00000003583 intron 1 r STPG1 ENSG00000001460
chr1 24696163 24696329 ENST00000003583 cds 2 r STPG1 ENSG00000001460
chr1 24696329 24700191 ENST00000003583 intron 2 r STPG1 ENSG00000001460

I have a colleague who made it but cannot remember how. Most columns are clear what they represent, and are relatively straightforward to obtain. What I'm having trouble with is column 6, which (e.g. 0, 1, 2), which represents the exon/intron index in sequence. Is there any database or file which contains this information?

exon • 817 views
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What kind of data do you have? Please, provide more informaion!

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Hi brunobsouzaa, The data that I have is in the above post. That is it. I need to know how to generate that file. It should be clear what each of the columns represent

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