Question: Downloadable File With Gene Locations
1
gravatar for anuragm
6.0 years ago by
anuragm130
India
anuragm130 wrote:

Is there a download-able file on UCSC database that gives the information on gene locations (the chromosome ID for the gene, and the base positions) for a given organism ? I want to know the distance (in bp) between certain genes of interest for Xenopus genome. Is there any other way to achieve this in the genome browser ?

gene annotation ucsc • 2.0k views
ADD COMMENTlink modified 6.0 years ago by PoGibas4.8k • written 6.0 years ago by anuragm130

start here: https://main.g2.bx.psu.edu/ import data from ucsc as GTF, filter for your gene names, do the statistics (?)

ADD REPLYlink written 6.0 years ago by Ido Tamir5.0k

The Downloads link is right there on the main UCSC page, left-hand column.

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by Neilfws48k
3
gravatar for PoGibas
6.0 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:
  1. Go to UCSC Genome Browser
  2. Select Tables
  3. Select clade and genome of interest (for example: vertebrate & X. tropicalis)
  4. Under group select "Genes and gene prediction tracks"
  5. Under track select whatever annotation you like (for example: RefSeq genes, Ensebml genes)
  6. Press "get ouput"

Wanted gene annotation provides: gene name, chrom, strand, txStart, txEnd, cdsStart, cdsEnd, exonCount, exonStarts. exonEnds.... and much more.

If you want to know the distance (in bp) between certain genes of interest you can use awk (I need your genes of interest and will provide an example how to compute them).

ADD COMMENTlink modified 6.0 years ago • written 6.0 years ago by PoGibas4.8k

Thanks a lot!

lets say I want to know the distance in bp between NM_001078816 and NM_001016199 on GL172637 (the first two genes in the RefSeq track for the Xenopus genome). I would be grateful if you show me how to go about it in awk. Thanks again!

ADD REPLYlink written 6.0 years ago by anuragm130
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