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• How to get promoter coordinates of hg19 from UCSC genome browser ?
  Hi all, I need to get Promoter coordinates of all genes in human genome from hg19 assembly. Is ...
• Snps In Promoter Regions In Exome Sequencing?
  I have on hand exome sequencing data. One question was posed to me in a biological standpoint tha...
• Retrieving promoter regions from ucsc using mysql
  Hello there, I think this is a really easy question for anybody with experience using mysql and...
• GFF3 to 12-column BED
  I am trying to get refseq annotation (txStart, txEnd, cdsStart, cdsEnd, exonStarts, exonsEnds etc...
• Getting Promoter Sequences (2Kb Upstream From Gene)
  Hi I have a list of genes (number is very huge). Is there any easy way to get the sequence of 2kb...
• List of well-separated hg19 genes (bed)
  I am trying to use deeptools to analyze ChIP-seq data to characterize elongation behavior of Pol ...
• Extracting promoter regions alignment
  Greetings, everyone! I`m trying to extract promoter regions alignment from UCSC Table Browser.  ...
• Intersecting unbalanced BED files, normalizing for one
  Have two bed files I am intersecting, one of approximately 500 promoters +/- 2kb of TSS and the o...
• How to use a specific promoter set on findMotifs.pl of HOMER?
  I want to get peaks of promoters of a list of genes using findMotifs.pl. findMotifs.pl $GENE...
• Bedtools intersect error in record file
  I keep getting an error with bedtools intersect when comparing a .bed file to a .gff, e.g. E...
• How O Assign A Color Ro Bed Regions (Ucsc)
  Hi, I am trying to assign a red color to my H3K4me1 peaks to upload into UCSC. I tried the follo...
• Help Please! Stuck in .bed format and need to convert for Impute2
  I started with PLINK data files, and changed the .map file over to the UCSC .bed format in order ...
• How Can I Extract All Bidirectional Promoters In The Human Genome From Ucsc Genome Browser?
  What I would like is a bed file of all regions which have two genes on opposite strands and the T...
• How to get the no-overlapping exome region (.bed file)?
  I want to get the hg38 whole exome regions (.bed) for the downstream analysis. However, some regi...
• Retrieve promoter sequences of all human genes
  Hi, I am hoping for some insight and suggestions concerning **retrieving promoter sequences:** ...