Any SQL or Perl script to do it?
• 0 views
•
link
written
by
Shicheng Guo
Where to download refseq gene data
3 answers
Download Human and Mouse refGene from UCSC with bash wget
wget -c -O mm9.refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/refGene.txt.gz
wget -c -O mm10.refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/refGene.txt.gz
wget -c -O hg19.refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/refGene.txt.gz
wget -c -O hg38.refGene.txt.gz http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz
BTW, they are same with hg19.refseq.bed12 when you use RSeQC to infer library type (unstranded or stranded )
infer_experiment.py -r knowngene.hg19.bed12 -i L007Aligned.sortedByCoord.out.bam
• 0 views
•
link
updated
by
Ram
•
written
by
Shicheng Guo
•
written
by
Shicheng Guo
This might work.
• 0 views
•
link
updated
by
Ram
•
written
by
KVC_bioinfo
•
written
by
KVC_bioinfo
Log in to answer this question.
More posts like this
-
gene transfer format in UCSC download
written by 897598644
-
Recurrent de novo mutation
written by 897598644
-
DNAssist for win7/win8 64 bit download
written by 897598644
-
DNAssist for win7/win8 64 bit download
written by 897598644
-
Variant filtering parameters
written by 897598644
-
Term of throughput in next generation sequencing
written by 897598644
-
Paired end sequencing and single end sequencing in next generation sequencing of Illumina platform
written by 897598644
-
1000 Genome Project and ESP for indel or frameshift
written by 897598644
-
how many bases in the number of inter-individual difference on average ?
written by 897598644
-
base quality in the result of mpileup
written by 897598644
Figure it out here: http://genome.ucsc.edu/cgi-bin/hgTables
I have downloaded the file. But the third column showed exon,CDS,start_codon and stop_codon regions. I wanted to got all exon and UTR regions coordinate. So is there a direct way to download the file without converting files like above?
If you click the 'describe table schema' button it will show you exactly what data will be in the downloaded file. The 'RefSeq Genes' table includes two comma-separated lists of exon start and exon end coordinates. It's relatively straightforward to take this and split it into a list of just exonic regions (in BED file format or something).