downloading promoter sequences using UCSC Table Browser
HI, I need to download 2000 upstream promoter region sequences of few genes but when i specify the gene along with its coordinates and chromosome the output sequence file i get contains all other coordinates of those genes except the one i mentioned in the input how do i download exact coordinate sequence file? please let me know
thankyou!!
• 1,199 views
•
link
written
by
ravi.eshwari •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to sync vcf file with the genome?
written by khanhlpbao •
-
Genome-wide enrichment of histone marks and correlation with gene expression: Approach/Tools?
written by Ankit
-
Get gene promoter coordinates
written by sabin •
-
Finding overlaps between GRanges objects
written by mickey_95 •
-
Nanopolish variant calling. Need to specify input region of the reference genome
written by SUDOsundu •
-
Extract coordinates of upstream region up to closest coding region in R
written by eggrandio •
-
Get -400bp to +50bp sequence of gene from gff3 file
written by Biogeek
-
How to compare the promoter region of same genes in pan-genome in a high-throughput way
written by jerrywu1987 •
-
Determine promoter regions relative to TSS.
written by robbenstijn •
-
Snps Which Are Present In Upstream Region Or Downstream Region?
written by Elena
You can simply obtain the coordinates of the entire gene and then use
bedtools slopto extend the start of the gene by a desired number of basepairs in upstream direction to get an approximation of the promoter sequence. Be sure to use it in a strand-specific fashion to respect the strand the gene is on.