Encode promoters

I am using encode promoters and UCSC promoters. For UCSC promoters I simply took 1000 bases upstream. Do I need to do that for encode promoters too that is subtract or add 1000 from their start or end position depending on the strand?

promoters encode ucsc

• 789 views • link

written 4.7 years ago by peter •

0 answers

No answers yet.

More posts like this

Should I look 1000 bases or 2000 bases upstream for promoters in humans
written 4.7 years ago by peter •

I am looking to download promoters bed file from both UCSC and CAGE. I am trying to look into papers to see whether people usually …
Extracting promotes from UCSC
written 4.7 years ago by peter •

I downloaded promoter bed file of humans from UCSC. I basically just looked 1000bases upstream and downloaded the bed file. However, when I did an …
Question regarding CAGE and UCSC promoters and enhancers
written 4.7 years ago by peter •

I have download a promoter bed file from UCSC. And I have a [promoter bed file][1] from CAGE. In case of UCSC I look 1000bases …
Confused about TSS coordinates
written 7.1 years ago by srhic •

Hello, I have a very basic question about the coordinates of TSS sites which I am a little confused about. I am trying to plot …
Extracting promoter sequence with GenomicFeatures ?
written 7.2 years ago by lokraj2003

I am trying to extract promoter sequence of a non-model organism (Orf virus). I used flank function from GenomicFeatures to extract 50 base pairs upstream …
How to annotate GAW18 SNPs using R
written 10.7 years ago by 379225693 •

Excuse me ,I am using a SNPs data which come from GAW18. I want to define a "group" of SNPs as the set of SNPs …
retrieving refseq/ucsc transcription start site with 1kb up- and downstream flank?
written 10.8 years ago by taniasultana2004 •

Hi! I need to plot some genomic locations in context of their distances from transcription start site, CpG islands and Dnase hypersensitive sites. Question1) Can …
How to script for adding and subtracting values to look upstream?
written 11.3 years ago by oliver.bayfield •

I have a file output from a tblastn search, in outformat 6 (tabular/ tab delimited), with the columns: subject gi, evalue, subject start, subject end. …
How To Find The Oriantation Of The Repeats Downloaded From Ucsc
written 12.6 years ago by roll

Hi, I downloaded the repeats from UCSC repeatMasker as fa.out files and converted them to bed files simply using awk. I am now trying to …
How To Find Nearest Gene Upstream Using Mysql And Perl Program
written 13.4 years ago by anon111 •

How to Find nearest gene upstream using mysql and perl program There is a table of genes in mysql. I have a list of reg. …