Table Browser refGene identifiers question

Question

[rbronste]

Hi,

I want to put a list of genes into table browser (identifiers tab) and get a BED file with whole gene intervals however when I input 10K gene names into Genes and Gene Predictions I get a file out with 17K intervals. Is there any straightforward way to keep it to the 10K genes only and not include the predictions as well? I am assuming thats where the additional numbers come from. Thanks.

Rob.

[Pierre Lindenbaum]

what kind of identifiers is it ? ucsc id ? ensembl-id ? common names ?

[rbronste]

Its common names I believe, those spit out by cuffdiff.

Answer 1

[Pierre Lindenbaum]

use mysql ucsc, something like:

$ join -t $'\t' -1 1 -2 4 <(cat geneids.txt | LC_ALL=C sort | uniq ) <(mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg19 -N -e 'select chrom,txStart,txEnd,name2  from wgEncodeGencodeBasicV7 limit 10' | LC_ALL=C sort -t $'\t' -k4,4 | uniq )