Question: Create Your Own Exon/Intron/Utr Bed File Similar To That Created By Ucsc Without Using Ucsc Browser
0
gravatar for skm770
6.4 years ago by
skm770150
skm770150 wrote:

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.

ucsc cds exon utr intron • 3.2k views
ADD COMMENTlink modified 6.4 years ago by Alex Reynolds30k • written 6.4 years ago by skm770150
3
gravatar for Alex Reynolds
6.4 years ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

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.

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Alex Reynolds30k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1645 users visited in the last hour