Create Your Own Exon/Intron/Utr Bed File Similar To That Created By Ucsc Without Using Ucsc Browser

Question

[skm770]

The genome that I am working on is not enlisted in the UCSC browser. Are there available tools that I can use to create the exon,intron and utr bed files that are produced by UCSC table browser. This is the format that UCSC produces :-

chr1    14361   14829   NR_024540_utr3_0_0_chr1_14362_r 0       -       NR_024540       WASH7P  653635  pseudogene
chr1    14969   15038   NR_024540_utr3_1_0_chr1_14970_r 0       -       NR_024540       WASH7P  653635  pseudogene
chr1    15795   15947   NR_024540_utr3_2_0_chr1_15796_r 0       -       NR_024540       WASH7P  653635  pseudogene
chr1    16606   16765   NR_024540_utr3_3_0_chr1_16607_r 0       -       NR_024540       WASH7P  653635  pseudogene
chr1    16857   17055   NR_024540_utr3_4_0_chr1_16858_r 0       -       NR_024540       WASH7P  653635  pseudogene
chr1    17232   17368   NR_024540_utr3_5_0_chr1_17233_r 0       -       NR_024540       WASH7P  653635  pseudogene
chr1    17605   17742   NR_024540_utr3_6_0_chr1_17606_r 0       -       NR_024540       WASH7P  653635  pseudogene
chr1    17914   18061   NR_024540_utr3_7_0_chr1_17915_r 0       -       NR_024540       WASH7P  653635  pseudogene
chr1    18267   18366   NR_024540_utr3_8_0_chr1_18268_r 0       -       NR_024540       WASH7P  653635  pseudogene

I was wondering if there are already available tools that I can use for my particular organism to start from gff3 file and get the above output.

Answer 1

[Alex Reynolds]

You might take a look at BEDOPS gff2bed for conversion of GFF3 input to extended BED, along with standard utilities like cut or awk for tweaking converted output.