Question: How To Get A List Of All Human Genes Above A Certain Length
1
gravatar for Whetting
4.7 years ago by
Whetting1.5k
Bethesda, MD
Whetting1.5k wrote:

Hi,
I want to assemble a list of human genes longer than a specified length.
Any ideas on how to accomplish such a feat? thanks!!

gene length human download • 1.8k views
ADD COMMENTlink modified 4.7 years ago by Ashutosh Pandey11k • written 4.7 years ago by Whetting1.5k
3
gravatar for Ashutosh Pandey
4.7 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

Try this command :

$ mysql --user=genome -N --host=genome-mysql.cse.ucsc.edu -A -D hg19  -e "select name,name2,txEnd - txStart from refGene"  > Gene_sizes.txt

You can sort Gene_sizes file now using length that is in the third column. The table includes all the Refseq transcripts for a gene. You can get multiple information from UCSC. See the table schema: http://genome.ucsc.edu/cgi-bin/hgTables

ADD COMMENTlink modified 4.7 years ago by Istvan Albert ♦♦ 75k • written 4.7 years ago by Ashutosh Pandey11k
1

I was about to paste this: to limit above 1000 bases and dispaly top 20:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -e ' select distinct name, chrom, txStart, txEnd, (txEnd - txStart) as length from refGene where (txEnd - txStart) > 1000 limit 20'
ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Rm7.6k
1

I'm curious if the OP wants this length (from transcription start to end) or the eventual length of the transcript generated (ie. the length after introns have been spliced out).

ADD REPLYlink written 4.7 years ago by Steve Lianoglou4.8k

Question was not specific: there are few ways to get the information: start to end; sum all the exon length in a transcript etc.

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by Rm7.6k
1

Simplest just to sort Swiss-Prot Human by protein size ?

ADD REPLYlink written 4.7 years ago by cdsouthan1.8k
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